Unix for Bioinformatics Beginners
ssh(connect to remote computer such as a high performance computing cluster)pwd(print working directory)cd(change directory)ls(list directory content)mkdir(make a directory)touch(creates an empty file)nano(basic editor for editing text files)cp(make a copy of files or folders)mv(rename files/folder or move files or folders)rm(to remove files or folders)cat(print file content to screen)less(page through file content)column(display tabular data nicely aligned on screen)wc(word count, line count and character count)grep(pattern search)sinteractive(request compute and time resources on Biowulf's compute node to perform data analysis and file transfers)module(find, load, and unload applications installed on high performance computing clusters)man(view manual for a command)
Tip
All Unix commands follow the syntax of command option(s) input. Think of the command as a verb in natural language. The input is what users would like the command to act on and option(s) changes the default way in which a command runs.
Connecting to Remote Computer
As bioinformatics often deal with dataset that are too large to be analyzed using compute resources on a personal computer, a motive for learning Unix command line is to enable scientists to perform bioinformatics analyses on high performance computing systems such as Biowulf at NIH. To connect to a remote computer, the ssh command construct below can be used and the breakdown is as follows.
ssh: The command for connecting to a remote computer.username: The user name that is used to sign onto a remote computer such as high performance computing (for Biowulf,usernamewill be the user's NIH user name). Username is followed by@(ie. the "at" symbol).remote: This is the name of the remote computer (Biowulf would bebiowulf.nih.gov) to connect to.
ssh username@remote.computer
The command above could be annunciated as ssh username at remote.computer.
To sign onto Biowulf, the NIH high performance computing system, use the following. Again, replace username with the user's NIH user name.
ssh username@biowulf.nih.gov
Next, enter the user specific password for the remote computer. Note that nothing shows up when the password is being type, but keep typing and hit enter when ready to sign on.
The Command Prompt
In Unix, the command prompt is where users issue commands to interact with the computer. For example, upon connecting to Biowulf, users will see the prompt shown below. Replace username with the user's NIH user name. The prompt below tells users that they are connected to Biowulf and are currently in the home directory (denoted by ~).
[username@biowulf ~]$
Caution
The prompt will look different depending on the computer system. It can also be customized, so do not panic if a prompt does not look exactly like that above.
Print the Working Directory
Definition
The working directory is the folder in a computer system in which a user is currently in.
It is a good idea to know which directory a user is currently in as data analysis progresses. To check, use the following.
pwd
For instance, upon signing on to Biowulf users will land in their home directory (also denoted by ~). The pwd command will give the directory path below (replace username with the user's specific user name).
/home/username
Note
In Unix, a directory path indicates where in the file system hierarchy a user is. Directory paths that start with / are known as absolute. Each part of the directory path is separated by / and followed by the name of the folder in the file system hierarchy.
Change Directory
Note
The user's home directory on Biowulf is not the place to store analysis input and output as it only has 16gb of storage space and users cannot request an increase in quota. The user's data directory can be used for this as storage quota can be increased at the request of the user.
To change directory use the cd command follow by the directory to change into. Upon signing onto Biowulf, users should change into their data directory to performing analyses. To do this use the following. Replace username with the user's specific user name.
cd /data/username
The pwd command can be used to check whether the directory change is successful.
pwd
If the directory change is successful, the following path will be shown, again replace username with the user's NIH user name.
/data/username
To go back to the user's home directory use cd, cd ~, or cd /home/username. Use cd .. to go back one directory. To go back two directories, use cd ../../. To go back three directories use cd ../../../ and so on.
Note
The examples below will be done using a folder called unix_demonstration in the instructor's /data folder. There is no need to follow along. To change into unix_demonstration from the /data folder, just do cd unix_demonstration.
Listing Directory Content
To view the files and subfolder within a directory, the ls command can be used. For instance, ls will retrieve the following items in the unix_demonstration directory when issued.
file.txt
Recall that a Unix command come with options that alter its default behavior. The -l option of ls gives a detailed view of each item in a directory. For instance, on the left hand column of the table below, lines that start with - are files while those starting with d are folders. The fifth column list the file or folder size. Note file.txt has a file size of 0 bytes since it is empty. Also, ls -l by default displays the files size in bytes.
-rw-r-----. 1 owner group 0 Jun 15 16:20 file.txt
Creating a New Directory
To make a new folder, use the mkdir command follow by the name of the folder.
mkdir folder
Recall
As mentioned previously, if the first column in the ls -l results starts with d then this indicates a directory, which is what folder should be.
ls -l
-rw-r-----. 1 owner group 0 Jun 16 10:09 file.txt
drwxr-x---. 2 owner group 4096 Jun 16 10:18 folder
Editing Files
Nano is a basic file editor that is built into Unix and enables editing of plain text files including txt, csv, fasta, genbank, gtf, and fastq. To edit a file using Nano, just use nano followed by the file name.
Unix is an operating system, just like Windows or MacOS.
Linux is a variety of Unix, and sometimes the names are used interchangeably.
For instance, to add the text above to file.txt, use:
nano file.txt
Then copy and paste the text into the editor. Hit control-x and then save to go back to the command prompt.
Note
If a file does not exist, then the nano command will create it as well as open the editor to enable editing. To create a blank file without opening the Nano editor, use the touch command instead.
touch bioinformatics.txt
ls -l
-rw-r-----. 1 owner group 0 Jun 16 18:13 bioinformatics.txt
-rw-r-----. 1 owner group 135 Jun 16 18:13 file.txt
drwxr-x---. 2 owner group 4096 Jun 16 10:18 folder
Copying Files and Folders
To copy a file use cp followed by the file name and the name of the duplicate.
For instance, to make a copy of bioinformatics.txt called btep_bioinformatics.txt, do:
cp bioinformatics.txt btep_bioinformatics.txt
ls
bioinformatics.txt btep_bioinformatics.txt file.txt folder
The cp command can be used to copy a file into a folder. Just provide the file and the path to the folder in which to copy it. If a new name is desired for the duplicate, then append it to the destination folder path separated by a /. For instance, the command below will make a duplicate of bioinformatics.txt in folder called bioinformatics_for_beginners.txt.
cp bioinformatics.txt folder/bioinformatics_for_beginners.txt
Tip
To see contents of a folder other than those in the working directory, supply the path to the folder to the ls command.
ls folder
bioinformatics_for_beginners.txt
To copy a folder include the -r option in cp. The -r option recursively copies everything in a folder. The arguments are the folder to copy and the name of the duplicate folder.
cp -r folder bioinformatics_folder
The -1 option of ls prints directory content one item per line.
ls -1
bioinformatics_folder
bioinformatics.txt
btep_bioinformatics.txt
file.txt
folder
ls bioinformatics_folder
bioinformatics_for_beginners.txt
Renaming Files and Folders
The mv command can be used to rename files and folders.
To rename a file, use the mv command then provide the name of the file to rename and the new name of the file.
mv btep_bioinformatics.txt bioinformatics_for_noobies.txt
ls -1
bioinformatics_folder
bioinformatics_for_noobies.txt
bioinformatics.txt
file.txt
folder
To rename a folder, use the mv command and then provide the name of the folder to rename and the new name of the folder.
mv folder project_folder
ls -1
bioinformatics_folder
bioinformatics_for_noobies.txt
bioinformatics.txt
file.txt
project_folder
Moving Files and Folders
To move a file from one folder to another, the mv command can be used. The arguments in this application of the mv command is the file to be moved and the name of the folder in which the file will be moved to.
mv bioinformatics.txt bioinformatics_folder
ls bioinformatics_folder
bioinformatics_for_beginners.txt bioinformatics.txt
Tip
mv can also move folders. Just supply the name of the folder to be moved as the first argument and the path of the destination folder.
Deleting Files and Folders
To delete a file use the rm command followed by the file name.
For instance, to delete bioinformatics_for_noobies.txt do:
rm bioinformatics_for_noobies.txt
Warning
There is no trash can or recycling bin in Unix. Once a file is deleted, it cannot be recovered. Use the -i option with rm to confirm deletion.
rm -i bioinformatics_for_noobies.txt
Type n for no and y for yes (to delete).
rm: remove regular empty file 'bioinformatics_for_noobies.txt'? n
Empty folders can be deleted using rmdir. On the other hand, folders with content can be removed using rm -r, where the -r option tells rm to delete the folder and recursively delete everything inside that folder.
rm -r -i project_folder
The command above will ask if the user wants to delete the project_folder and everything in it. Type y to confirm deletion. Users will be asked to confirm the deletion of each item in the folder.
rm: descend into directory 'project_folder'? y
rm: remove regular empty file 'project_folder/bioinformatics_for_beginners.txt'? y
rm: remove directory 'project_folder'? y
ls -1
bioinformatics_folder
bioinformatics_for_noobies.txt
file.txt
Viewing File Content
The cat command will print the entire content of a file to the terminal screen.
For instance, to view the content of file.txt in the terminal screen do:
cat file.txt
Unix is an operating system, just like Windows or MacOS.
Linux is a variety of Unix, and sometimes the names are used interchangeably.
The cat command can also be used to view fastq or fq files, which contain sequences from high throughput sequencers. For long files that take a while to completely print, hit control-c to exit the cat command and return to the prompt.
cat example_fastq.fq
Tabular data in the form of csv files can be displayed by cat as well.
cat example_rna_sequencing_counts.csv
Paging through Files
Rather than printing file content in its entirety to the terminal, users can page through files using less.
less example_rna_sequencing_counts.csv
Users can use the up and down arrow on the keyboard to scroll up/down the file to view content. The up/down arrows enable scrolling line by line.
Printing Tabular Data to Terminal Nicely Aligned
For tabular data in the form of csv files, which could contain multiple columns, the columns do not print to the terminal nicely aligned. The column command can fix this.
The options and arguments in the column command include:
- Option
-t: Creates a table. - Option
-s: Prompts users to provide the column separator (ie. comma for csv files) - Argument: Name of the file which users would like to view (ie. example_rna_sequencing_counts.csv)
|is the pipe operator, which sends output from one command as input for another (ie.lessto enable paging through the data table)
column -t -s ',' example_rna_sequencing_counts.csv | less
column command outputGeneid HBR_1.bam HBR_2.bam HBR_3.bam UHR_1.bam UHR_2.bam UHR_3.bam
U2 0 0 0 0 0 0
CU459211.1 0 0 0 0 0 0
CU104787.1 0 0 0 0 0 0
BAGE5 0 0 0 0 0 0
ACTR3BP6 0 0 0 0 0 0
5_8S_rRNA 0 0 0 0 0 0
AC137488.1 0 0 0 0 0 0
AC137488.2 0 0 0 0 0 0
CU013544.1 0 0 0 0 0 0
CT867976.1 0 0 0 0 0 0
CT867977.1 0 0 0 0 0 0
CT978678.1 0 0 0 0 0 0
CU459202.1 0 0 0 0 0 0
AC116618.1 0 0 0 0 0 0
CU463998.1 0 0 0 0 0 0
CU463998.3 0 0 0 0 0 0
CU463998.2 0 0 0 0 0 0
U6 0 0 0 0 0 0
LA16c-60D12.1 0 0 0 3 2 0
LA16c-13E4.3 0 0 0 0 0 1
LA16c-60D12.2 0 0 0 0 4 1
ZNF72P 0 0 0 0 1 0
BNIP3P2 0 0 0 0 2 0
YME1L1P1 0 0 0 0 0 0
OR11H1 0 0 0 0 0 0
LA16c-60G3.6 0 0 0 0 3 0
ARHGAP42P3 0 0 0 0 2 0
LA16c-23H5.4 0 0 0 0 1 0
LA16c-60G3.8 0 0 0 0 2 0
LA16c-60G3.7 0 0 0 0 0 0
LA16c-60G3.5 0 0 0 0 0 0
LA16c-2F2.8 0 0 0 0 3 0
NEK2P2 0 0 0 0 1 1
LA16c-2F2.5 0 0 0 0 0 0
NF1P6 0 0 0 1 4 0
MED15P7 0 0 0 0 2 0
POTEH 0 0 1 7 7 11
POTEH-AS1 0 0 0 0 2 0
RNU6-816P 0 0 0 0 0 0
LA16c-3G11.7 0 0 0 2 1 2
LA16c-83F12.6 0 0 0 3 1 0
GRAMD4P2 0 0 0 0 1 0
DUXAP8 10 4 9 250 199 213
LL22NC03-N64E9.1 0 1 0 16 9 19
BMS1P22 0 1 3 25 24 24
LL22NC03-N14H11.1 4 2 0 98 38 49
NBEAP3 0 0 0 5 3 0
LA16c-60H5.7 0 0 0 11 6 6
LA16c-4G1.4 0 0 0 0 0 0
LA16c-4G1.3 0 0 0 0 3 0
AC092854.1 0 0 0 0 0 0
ABCD1P4 0 0 0 0 2 0
LA16c-17H1.3 0 0 0 0 0 0
PABPC1P9 0 0 0 0 1 0
SLC9B1P4 0 0 0 0 1 0
ACTR3BP2 0 0 0 0 0 0
CHEK2P4 0 0 0 0 0 0
KB-67B5.17 0 0 0 0 0 0
KB-67B5.12 0 0 0 0 0 0
KCNMB3P1 0 0 0 2 1 1
CCT8L2 0 0 0 1 2 0
FABP5P11 0 0 0 0 0 0
AP000547.1 0 0 0 0 1 0
TPTEP1 19 23 20 141 94 122
KB-7G2.9 0 0 1 3 4 2
SLC25A15P5 0 0 0 2 2 4
PARP4P3 0 0 0 1 1 2
ANKRD62P1-PARP4P3 0 1 0 3 3 0
ANKRD62P1 0 0 0 2 0 1
KB-7G2.8 0 0 0 0 0 0
VWFP1 2 2 4 1 2 0
AC005301.8 0 0 0 1 0 0
XKR3 0 0 0 3 4 8
HSFY1P1 0 0 0 0 0 0
GPM6BP3 0 0 0 0 0 0
AC007064.22 0 0 0 0 0 0
ZNF402P 0 0 0 1 1 0
AC007064.24 1 3 2 3 0 1
MTND1P17 0 0 0 0 0 0
AC007064.25 0 0 0 0 0 0
AC006548.19 0 0 0 0 0 0
IGKV1OR22-5 0 0 0 0 0 0
IGKV2OR22-4 0 0 0 0 0 0
IGKV2OR22-3 0 0 0 0 0 0
IGKV3OR22-2 0 0 0 0 1 0
IGKV1OR22-1 0 0 0 0 0 0
AC006548.28 1 1 1 4 40 4
GAB4 0 0 0 0 0 0
AC006548.26 0 0 0 0 0 0
VN1R9P 0 0 0 0 0 0
CECR7 22 27 32 31 27 24
AC006946.16 7 6 4 3 3 4
AC006946.17 0 2 2 0 3 2
IL17RA 58 65 58 95 71 81
AC006946.12 0 1 1 1 1 1
CECR6 26 45 32 9 6 4
AC006946.15 3 3 1 0 2 0
CECR5 30 44 33 127 82 139
CECR5-AS1 0 2 2 1 2 1
CECR1 30 28 32 39 35 22
AC005300.5 0 0 0 1 0 0
FAM32B 0 1 0 0 0 0
CECR3 1 0 1 0 1 0
CECR9 0 0 0 0 0 0
RN7SL843P 0 0 0 0 0 0
CECR2 115 88 119 119 81 98
AC004019.10 1 5 1 0 1 1
CLCP1 1 2 0 0 0 0
DNAJA1P6 0 0 0 0 0 0
SLC25A18 100 111 74 6 8 7
AC004019.13 1 2 1 1 2 3
ATP6V1E1 392 454 391 244 181 203
BCL2L13 212 284 264 244 166 200
BID 70 85 84 112 76 109
MIR3198-1 0 0 0 0 0 1
LINC00528 1 0 0 1 2 4
MICAL3 339 429 425 211 145 193
XXbac-B461K10.4 6 6 9 1 2 1
MIR648 0 0 6 0 0 0
XXbac-B476C20.14 2 7 2 2 1 1
XXbac-B476C20.13 2 9 4 1 2 3
RHEBP3 1 2 3 0 0 1
FLJ41941 0 0 0 0 2 0
XXbac-B476C20.9 3 5 4 2 3 5
PEX26 135 174 137 205 135 180
XXbac-B476C20.11 0 0 1 3 0 0
XXbac-B476C20.10 0 0 0 0 0 0
ARL2BPP10 0 0 0 0 0 0
TUBA8 13 13 15 2 2 1
AC008079.10 55 68 53 14 14 8
USP18 3 6 2 28 14 21
AC008079.9 0 0 0 0 0 0
GGTLC5P 0 0 0 0 0 0
AC011718.2 1 0 0 0 0 0
AC011718.3 0 0 0 0 0 0
PPP1R26P3 0 0 0 0 0 0
XXbac-B33L19.6 0 0 0 0 0 0
FAM230A 0 0 0 2 4 0
XXbac-B33L19.12 0 0 0 0 0 0
GGTLC3 0 0 0 0 0 0
Metazoa_SRP 0 0 1 0 2 2
XXbac-B33L19.15 0 0 0 0 0 0
TMEM191B 6 1 3 0 2 2
PI4KAP1 18 11 36 65 33 34
SCARNA17 0 0 0 0 0 0
RN7SKP131 0 0 0 0 0 0
RIMBP3 1 2 0 2 3 6
XXbac-B33L19.10 0 0 0 0 0 0
CA15P2 0 0 0 0 0 0
PPP1R26P2 0 0 0 0 0 0
PPP1R26P4 0 0 0 0 0 0
AC008132.15 0 0 0 0 1 0
GGT3P 0 0 0 0 0 1
AC008132.14 0 0 0 0 0 0
E2F6P1 0 0 0 3 0 0
AC008132.13 0 0 1 1 3 1
BCRP7 0 0 0 0 0 0
AC008103.3 0 0 0 0 0 0
AC008103.4 0 0 0 0 0 0
DGCR6 73 91 76 24 13 18
PRODH 102 127 123 44 34 39
AC007326.1 0 0 0 3 1 3
AC007326.10 0 1 0 0 3 0
DGCR5 196 239 201 8 9 8
AC007326.9 11 9 12 1 0 0
DGCR9 30 30 27 5 2 4
AC000095.9 0 0 0 0 0 0
AC000095.11 9 5 9 0 0 0
CA15P1 4 3 5 1 2 1
DGCR2 304 354 314 308 178 274
Y_RNA 4 2 2 5 2 3
DGCR11 4 10 13 19 6 14
AC004461.4 1 1 0 0 2 0
DGCR12 2 1 7 2 2 4
AC004471.9 5 4 5 4 3 5
AC004471.10 1 1 0 0 2 0
TSSK1A 0 0 0 0 2 1
DGCR14 46 50 37 77 39 64
TSSK2 0 0 0 0 0 0
GSC2 0 0 0 0 0 0
LINC01311 3 1 3 11 8 11
SLC25A1 32 50 41 226 138 216
CLTCL1 33 40 36 102 71 81
AC000081.2 0 0 1 0 1 0
SNORA15 0 0 0 0 1 0
KRT18P62 1 1 0 1 0 1
HIRA 20 15 10 59 27 39
C22orf39 64 74 76 100 88 90
RN7SL168P 0 1 0 4 2 1
MRPL40 29 36 31 113 70 91
AC000068.5 5 4 1 6 8 5
UFD1L 38 58 53 228 148 168
AC000068.9 0 0 0 0 0 0
AC000068.10 0 0 0 0 2 4
CDC45 2 1 0 224 154 175
CLDN5 60 86 57 2 2 0
LINC00895 0 0 0 0 0 0
AC000077.2 0 0 0 0 1 0
AC000067.1 0 0 0 0 0 0
SEPT5 481 635 547 145 97 110
GP1BB 0 0 0 0 0 0
TBX1 1 0 2 7 9 7
GNB1L 14 17 8 39 36 30
AC000089.3 1 0 0 2 1 1
C22orf29 83 123 95 211 149 168
TXNRD2 55 52 41 84 68 74
AC000078.5 2 9 2 8 4 4
COMT 96 113 87 205 111 166
MIR4761 0 0 1 1 0 0
ARVCF 143 157 135 86 35 52
TANGO2 36 47 38 68 48 43
MIR185 0 0 0 0 0 0
AC006547.13 7 17 15 13 9 16
AC006547.15 0 0 0 0 0 0
DGCR8 80 96 67 238 162 203
MIR3618 0 0 0 0 0 0
MIR1306 0 0 0 0 0 0
AC006547.8 0 0 0 0 0 0
TRMT2A 42 62 49 164 82 128
MIR6816 0 0 0 0 0 0
RANBP1 52 74 70 593 399 475
SNORA77 0 0 0 0 0 0
ZDHHC8 95 97 91 114 84 82
AC006547.14 6 5 4 3 3 2
XXbac-B444P24.8 0 1 3 0 0 0
LINC00896 0 3 0 7 4 7
RTN4R 74 93 84 19 11 11
MIR1286 1 3 0 0 0 0
XXbac-B444P24.10 1 1 0 1 4 0
DGCR6L 47 42 38 96 46 86
XXbac-B444P24.13 1 2 3 2 1 4
XXbac-B444P24.14 3 3 3 3 0 2
XXbac-B33L19.4 0 0 0 1 0 0
USP41 0 0 0 3 2 0
ZNF74 38 40 41 110 79 90
RNU6-225P 0 0 0 0 0 0
SCARF2 11 7 2 34 23 38
XXbac-B562F10.12 0 0 0 0 0 0
KLHL22 63 80 83 81 52 65
XXbac-B562F10.11 4 8 13 10 5 3
RNY1P9 0 0 0 0 0 0
RN7SL812P 0 0 3 1 0 3
KRT18P5 4 3 1 4 2 8
AC007731.1 0 0 0 0 0 0
MED15 94 110 87 258 156 210
AC007050.17 0 0 0 3 2 2
AC007050.18 0 0 1 0 0 0
SMPD4P1 2 4 2 1 3 1
IGLL4P 0 0 0 0 1 0
SLC9A3P2 0 0 0 0 0 2
AC007050.1 0 0 0 0 0 0
ABHD17AP4 0 1 3 0 2 3
POM121L4P 0 0 0 0 1 0
BCRP5 0 0 0 0 0 0
TMEM191A 5 7 5 0 4 6
PI4KA 1102 1211 1079 433 343 391
SERPIND1 13 11 8 158 109 124
SNAP29 33 48 44 114 82 76
AC007308.7 0 0 0 0 0 0
CRKL 343 423 367 758 482 613
XXbac-B135H6.15 5 3 4 1 6 0
AIFM3 85 82 100 7 13 10
LZTR1 140 179 126 297 188 223
XXbac-B135H6.18 4 5 1 1 2 1
THAP7 36 56 39 95 77 87
THAP7-AS1 4 7 6 9 2 4
TUBA3FP 2 1 2 6 6 5
P2RX6 35 33 31 23 19 27
SLC7A4 19 25 14 9 4 3
AC002472.11 0 0 1 0 0 0
MIR649 0 0 0 0 0 1
P2RX6P 5 2 2 0 1 2
LRRC74B 0 2 2 1 1 1
TUBA3GP 0 0 0 0 0 0
BCRP2 1 0 0 0 1 0
KB-1592A4.15 0 0 0 0 0 0
POM121L7 1 0 1 0 0 0
E2F6P2 0 1 0 0 0 0
FAM230B 0 0 0 0 1 0
KB-1592A4.14 0 0 0 0 0 0
GGT2 0 0 1 3 2 0
E2F6P3 0 0 0 0 0 0
POM121L8P 0 0 0 0 0 0
BCRP6 0 0 0 0 0 0
KB-1183D5.13 0 0 0 0 0 0
KB-1183D5.14 0 0 0 0 0 0
PPP1R26P5 0 0 0 0 1 0
KB-1183D5.18 0 0 0 0 0 0
KB-1183D5.16 0 0 0 0 0 0
RIMBP3B 0 1 0 0 2 2
RN7SKP63 0 0 0 0 0 0
HIC2 29 25 28 209 106 140
TMEM191C 1 1 6 1 5 3
PI4KAP2 28 26 20 96 60 67
RN7SKP221 0 0 0 0 0 0
RIMBP3C 0 0 0 0 1 0
UBE2L3 207 241 198 470 310 346
YDJC 18 28 24 155 83 125
CCDC116 2 0 1 5 3 2
KB-1440D3.14 0 0 0 2 1 1
SDF2L1 5 14 3 51 34 44
PPIL2 60 65 60 243 146 211
MIR301B 0 0 0 0 0 0
MIR130B 0 0 0 0 0 0
KB-1440D3.13 0 0 0 4 5 1
YPEL1 25 45 31 17 9 8
RN7SL280P 1 0 1 1 1 0
MAPK1 741 955 901 840 502 664
RNA5SP493 0 0 1 3 4 1
KB-1027C11.4 0 1 1 1 0 1
PPM1F 80 106 108 217 140 169
LL22NC03-86G7.1 26 50 28 69 74 70
TOP3B 2 0 1 12 10 7
PRAMENP 0 0 0 0 0 0
IGLVI-70 0 0 0 0 1 0
IGLV4-69 0 0 0 0 0 0
IGLVI-68 0 0 0 0 0 0
LL22NC03-23C6.13 0 0 0 0 1 0
LL22NC03-23C6.12 0 0 0 0 1 0
IGLV10-67 0 0 0 0 0 0
LL22NC03-23C6.15 0 0 0 0 0 0
IGLVIV-66-1 0 0 0 0 0 0
IGLVV-66 0 0 0 0 0 0
IGLVIV-65 0 0 0 0 0 0
IGLVIV-64 0 0 0 0 0 0
IGLVI-63 0 0 0 0 1 0
IGLV1-62 0 0 0 0 2 0
LL22NC03-88E1.18 0 0 0 0 0 0
IGLV8-61 0 0 0 0 0 0
LL22NC03-88E1.17 0 0 0 0 0 0
ABHD17AP5 0 0 0 0 0 0
LL22NC03-30E12.10 0 0 0 0 0 0
LL22NC03-30E12.11 0 0 0 0 0 0
IGLV4-60 0 0 0 0 0 0
LL22NC03-30E12.13 0 0 0 0 0 0
SOCS2P2 0 0 0 0 1 0
IGLVIV-59 0 0 0 0 0 0
IGLVV-58 0 0 0 0 0 0
BMP6P1 0 0 0 0 0 0
IGLV6-57 0 0 0 1 0 0
IGLVI-56 0 0 0 0 0 0
IGLV11-55 0 0 0 0 0 0
IGLV10-54 0 0 0 0 0 0
IGLVIV-53 0 0 0 0 1 0
TOP3BP1 0 0 0 1 0 2
LL22NC03-123E1.5 0 0 0 0 1 0
VPREB1 0 0 0 1 0 1
CH17-264L24.1 12 12 18 16 15 13
LL22NC03-2H8.5 2 0 1 2 6 0
LL22NC03-2H8.4 0 0 0 0 0 0
LL22NC03-80A10.6 9 11 3 10 3 13
BMS1P20 3 1 7 6 1 2
IGLV5-52 1 2 3 0 0 0
IGLV1-51 1 4 1 0 1 0
IGLV1-50 1 3 0 0 0 0
LL22NC03-80A10.11 0 0 0 0 1 0
IGLV9-49 0 0 0 0 1 0
LL22NC03-75A1.9 0 0 0 0 0 0
IGLV5-48 0 0 0 0 0 0
IGLV1-47 0 0 0 0 0 0
LL22NC03-22A12.9 0 0 0 0 1 0
IGLV7-46 0 0 0 0 0 0
LL22NC03-22A12.12 0 0 0 0 0 0
IGLV5-45 0 0 0 0 0 0
IGLV1-44 0 0 0 0 0 0
IGLV7-43 0 0 0 0 0 0
IGLVI-42 0 0 0 0 0 0
IGLVVII-41-1 0 0 0 0 0 0
IGLV1-41 0 0 0 0 0 0
IGLV1-40 0 0 0 0 1 0
ASH2LP1 0 0 0 0 0 0
IGLVI-38 0 0 0 0 1 0
IGLV5-37 0 0 0 0 0 0
IGLV1-36 0 0 0 0 1 0
KB-288A10.17 0 1 0 0 1 0
IGLV7-35 0 0 0 0 0 0
KB-288A10.19 0 0 1 0 1 0
ZNF280B 28 37 39 65 55 42
ZNF280A 0 0 0 11 11 14
PRAME 0 0 0 822 472 606
LL22NC03-63E9.3 0 0 0 1 1 0
IGLV2-34 0 0 0 0 0 0
IGLV2-33 0 0 0 0 0 0
IGLV3-32 0 0 0 0 0 0
IGLV3-31 0 0 0 0 1 0
IGLV3-30 0 0 0 0 0 0
BCRP4 0 0 0 0 0 0
POM121L1P 0 0 0 0 1 0
GGTLC2 0 0 0 0 1 0
IGLV3-29 0 0 0 0 1 0
AC244250.2 0 0 0 0 0 0
IGLV2-28 0 0 0 0 0 0
IGLV3-27 0 0 0 2 0 0
IGLV3-26 0 0 0 0 0 0
IGLVVI-25-1 0 0 0 0 0 0
IGLV3-25 0 0 0 0 2 0
LL22NC03-102D1.16 0 0 0 0 0 0
LL22NC03-102D1.18 0 0 0 0 0 0
IGLV3-24 0 0 0 0 0 0
IGLV2-23 0 0 0 0 0 0
AC244250.1 0 0 0 0 0 0
IGLVVI-22-1 0 0 0 0 0 0
IGLV3-22 0 0 0 0 0 0
IGLV3-21 0 0 0 0 0 0
IGLVI-20 0 0 0 0 0 0
IGLV3-19 0 0 0 0 1 0
LL22NC03-48A11.14 0 0 0 0 0 0
AC244250.4 0 0 0 0 0 0
IGLV2-18 0 0 0 0 0 0
IGLL5 0 0 0 1 0 0
IGLV3-17 0 0 0 0 0 0
IGLV3-16 0 0 0 0 0 0
IGLV3-15 0 0 0 0 0 0
AC244250.3 0 0 0 0 0 0
IGLV2-14 0 0 0 26 12 13
IGLV3-13 0 0 0 0 0 0
IGLV3-12 0 0 0 0 0 0
LL22NC03-24A12.8 0 0 0 0 0 0
LL22NC03-24A12.9 0 0 0 0 0 0
AC244157.1 0 0 0 0 0 0
IGLV2-11 0 0 0 0 0 0
LL22NC03-84E4.13 0 0 0 0 0 0
IGLV3-10 0 0 0 0 0 0
LL22NC03-84E4.11 0 0 0 0 0 0
IGLV3-9 0 0 0 0 1 0
IGLV2-8 0 0 0 0 1 0
MIR650 0 0 0 0 0 0
LL22NC03-84E4.8 0 0 0 0 1 0
IGLV3-7 0 0 0 0 0 0
IGLV3-6 0 0 0 0 0 0
AC245028.1 0 0 0 0 0 0
IGLV2-5 0 0 0 0 0 0
IGLV3-4 0 0 0 0 0 0
IGLV4-3 0 0 0 0 0 0
IGLV3-2 0 0 0 0 0 0
IGLV3-1 0 0 0 0 0 0
MIR5571 0 0 0 0 0 0
IGLJ1 0 0 0 0 0 0
IGLC1 0 0 0 0 0 0
IGLJ2 0 0 0 0 0 0
IGLC2 0 0 0 706 503 534
IGLJ3 0 0 0 0 1 0
IGLC3 0 0 0 1170 317 803
IGLJ4 0 0 0 0 0 0
IGLC4 0 0 0 0 0 0
IGLJ5 0 0 0 0 1 0
IGLC5 0 0 0 0 0 0
IGLJ6 0 0 0 0 0 0
IGLC6 0 0 0 2 1 2
IGLJ7 0 0 0 0 0 0
IGLC7 0 0 0 8 5 5
AP000361.2 0 0 0 0 0 0
AP000362.1 0 0 0 1 0 0
RSPH14 4 8 5 1 0 0
GNAZ 223 247 214 32 17 26
AC000029.1 0 1 0 0 0 0
U7 0 0 0 0 0 0
RAB36 29 30 33 20 15 17
BCR 228 357 302 332 204 270
BCRP8 0 1 0 0 0 0
RN7SL263P 1 1 0 1 0 2
FBXW4P1 2 4 5 8 6 10
AP000343.1 0 2 0 0 0 0
AP000343.2 0 0 1 0 0 0
CES5AP1 2 2 0 0 1 0
ZDHHC8P1 21 16 14 1 2 3
KB-1269D1.8 1 1 0 0 0 0
AP000344.3 0 0 0 0 1 1
AP000344.4 0 1 0 1 3 1
AP000345.1 0 0 1 0 1 0
AP000345.4 0 0 0 4 4 3
PCAT14 0 0 1 202 156 181
AP000345.2 0 0 0 0 2 0
IGLL1 0 0 0 0 0 2
KB-208E9.1 1 3 1 0 1 0
KB-1572G7.5 0 1 0 1 1 0
DRICH1 2 2 1 0 4 2
KB-1572G7.4 0 0 1 0 0 1
KB-1572G7.3 0 3 0 0 0 1
GUSBP11 1 0 1 1 0 1
AP000347.4 0 0 0 1 5 1
ASLP1 1 1 2 5 3 4
KB-1572G7.2 0 0 1 0 0 1
AP000347.2 4 4 8 12 8 4
RGL4 16 27 18 17 15 8
ZNF70 26 46 32 80 48 41
VPREB3 0 0 0 0 0 3
C22orf15 2 7 7 4 3 6
CHCHD10 44 53 39 46 36 48
MMP11 3 1 1 15 17 17
AP000349.2 0 0 0 0 0 0
SMARCB1 70 78 62 169 131 139
DERL3 4 8 7 81 43 75
KB-1125A3.11 0 3 0 1 0 2
SLC2A11 54 63 46 28 34 27
AP000350.10 0 0 0 0 0 0
KB-1125A3.12 4 4 1 8 5 6
RN7SL268P 1 1 1 4 1 2
MIF 3 3 3 3 1 1
MIF-AS1 5 1 5 8 11 12
AP000350.5 11 14 12 30 24 27
AP000350.1 0 0 0 0 0 0
AP000350.6 2 2 1 3 1 7
AP000350.7 0 0 0 0 0 0
AP000350.8 0 0 0 0 0 0
GSTT2B 3 4 3 10 4 6
KB-1125A3.10 0 0 0 0 0 0
DDTL 3 3 3 2 17 5
KB-226F1.2 1 2 1 1 4 3
DDT 4 5 4 18 8 13
AP000351.3 0 0 0 0 0 0
GSTT2 0 0 0 0 0 0
AP000351.4 0 0 0 1 0 0
GSTTP1 0 0 0 0 1 1
AP000351.13 0 0 0 0 1 0
CABIN1 280 320 309 509 296 374
KB-318B8.7 13 11 7 14 10 13
SUSD2 8 8 7 11 17 10
GGT5 22 31 23 10 4 3
AP000354.4 0 0 1 0 0 0
POM121L9P 1 1 2 0 1 1
BCRP1 0 0 0 0 0 0
AP000354.2 0 0 0 0 1 0
SPECC1L 64 80 70 156 82 101
SPECC1L-ADORA2A 0 1 0 0 1 2
ADORA2A 2 4 2 4 0 0
ADORA2A-AS1 2 5 5 6 12 4
UPB1 0 1 2 1 10 2
AP000355.2 0 0 0 0 1 0
GUCD1 62 62 62 384 214 290
SNRPD3 71 87 98 293 211 254
GGT1 9 14 13 86 42 61
LRRC75B 20 30 26 21 24 24
AP000356.2 0 0 0 0 0 0
BCRP3 2 1 2 5 5 8
POM121L10P 0 0 0 0 0 0
ARL5AP4 0 0 0 0 0 0
AP000357.4 0 0 0 0 1 0
LL22NC03-N95F10.1 0 0 0 0 0 0
AP000358.5 0 0 0 0 0 0
CRIP1P4 0 0 0 0 1 0
PIWIL3 0 0 0 1 3 0
SGSM1 151 187 161 5 8 7
SNORD56 0 0 1 0 0 0
TMEM211 0 0 1 0 1 0
KIAA1671 126 148 131 158 97 142
CTA-243E7.4 3 3 0 1 3 0
CTA-243E7.3 0 1 1 1 1 0
CTA-243E7.2 0 2 1 4 4 3
CTA-243E7.1 5 6 3 12 19 6
CTA-221G9.12 7 7 6 4 1 1
CTA-221G9.10 0 0 0 0 0 0
CRYBB3 0 1 1 1 0 0
CTA-221G9.7 0 1 0 0 0 0
CRYBB2 0 1 0 0 4 0
Z99916.1 0 0 0 0 0 0
CTA-221G9.11 0 0 0 0 0 0
RP3-462D8.2 0 0 0 0 1 0
IGLL3P 0 0 0 0 0 0
CTA-246H3.8 0 1 0 2 2 1
CTA-246H3.11 0 2 2 4 2 1
LRP5L 7 5 5 41 24 26
CTA-246H3.12 0 0 0 1 2 1
CTA-390C10.9 0 1 0 0 0 2
IGLVIVOR22-1 0 0 0 0 0 0
CRYBB2P1 24 27 23 54 37 54
MIR6817 0 0 0 0 0 0
CTA-390C10.10 10 18 11 12 8 4
AL008721.1 0 0 0 0 0 0
CTA-407F11.8 1 1 0 1 2 1
ADRBK2 206 283 260 170 134 129
CTA-407F11.7 0 0 1 2 3 5
YES1P1 3 5 4 9 4 4
RNA5SP494 0 0 0 0 0 0
MYO18B 0 0 0 86 85 66
CTA-407F11.9 0 0 0 2 1 3
CTA-125H2.2 0 0 0 1 6 4
Z98949.1 0 0 0 1 1 0
CTA-125H2.1 0 0 0 0 0 0
RN7SKP169 0 0 0 0 1 0
CTA-125H2.3 0 0 0 0 0 0
CTA-796E4.3 0 0 0 0 1 0
CTA-796E4.4 1 0 0 0 1 1
SEZ6L 399 508 463 16 17 22
RP11-259P1.1 3 5 2 0 0 0
RNA5SP495 0 0 0 0 0 0
CTB-1048E9.7 0 0 0 0 1 0
ASPHD2 44 56 80 18 13 24
HPS4 114 176 183 318 202 256
SRRD 35 37 43 62 47 51
TFIP11 60 93 52 141 77 96
CTA-445C9.14 14 23 13 27 13 17
TPST2 38 39 38 85 46 85
MIR548J 0 0 0 2 0 0
HMGB1P10 2 3 2 9 10 6
CRYBB1 2 0 1 3 3 4
CRYBA4 1 0 0 0 1 1
ISCA2P1 0 0 0 0 1 0
MIAT 429 453 443 43 34 35
MIAT_exon1 0 0 0 0 0 0
CTA-373H7.7 0 4 0 0 0 0
MIAT_exon5_1 0 0 0 0 0 0
MIAT_exon5_2 0 0 0 0 0 0
MIATNB 4 6 8 11 14 12
MIAT_exon5_3 0 0 0 0 0 0
LINC01422 2 4 6 3 9 2
RP1-40G4P.1 0 0 0 0 0 0
CTA-992D9.11 0 0 0 0 8 0
RNU6-1066P 0 0 0 0 0 0
CTA-992D9.10 0 0 0 0 0 0
CTA-992D9.9 0 0 0 0 0 0
CTA-992D9.6 1 0 0 0 2 0
CTA-992D9.8 0 0 0 1 4 0
CTA-992D9.7 0 0 0 0 1 0
CTA-503F6.2 0 0 0 0 1 0
RP5-1172A22.1 1 0 0 2 1 3
CTA-929C8.5 0 0 0 0 0 0
CTA-929C8.7 0 0 0 0 0 0
CTA-929C8.6 0 0 0 0 3 0
CTA-929C8.8 1 3 1 0 0 0
RP1-205F14P.1 0 0 0 1 0 0
RP11-46E17.6 0 0 0 0 0 0
RP1-231P7P.1 0 0 0 0 2 0
RP1-213J1P__B.1 0 0 0 2 1 1
RP1-213J1P__B.2 0 0 0 0 0 0
RP11-375H17.1 0 0 0 0 1 0
MN1 44 34 31 123 93 124
PITPNB 80 92 64 111 87 87
TTC28-AS1 42 51 66 48 46 48
TTC28-AS1_1 0 0 0 0 0 0
MIR3199-2 1 0 0 1 0 1
TTC28-AS1_2 0 0 0 0 0 0
TTC28 87 123 79 191 108 106
TTC28-AS1_3 0 0 0 0 0 0
TTC28-AS1_4 0 0 0 0 0 0
RN7SL757P 1 0 0 0 0 0
SNORD42 0 0 0 0 0 0
MIR5739 0 0 1 3 2 2
RN7SL162P 0 0 0 0 0 1
CHEK2 1 5 3 98 82 99
HSCB 7 9 11 35 20 18
CCDC117 68 75 58 259 176 175
XBP1 67 102 79 1082 636 767
Z93930.1 0 0 0 1 0 1
CTA-292E10.6 4 7 2 10 12 16
CTA-292E10.8 1 0 0 4 3 2
CTA-292E10.7 0 0 0 0 0 0
ZNRF3 97 103 102 99 89 83
ZNRF3-IT1 1 6 3 4 3 2
ZNRF3-AS1 6 3 3 8 2 2
C22orf31 0 2 0 0 1 0
KREMEN1 50 62 36 75 59 69
CTA-747E2.10 1 0 2 0 0 0
Z95116.1 0 0 0 0 0 0
RNU6-810P 1 0 0 0 0 0
RNU6-1219P 0 0 0 0 0 0
EMID1 11 19 29 12 6 7
RHBDD3 23 40 33 79 57 67
CTA-984G1.5 2 1 3 9 3 5
EWSR1 346 356 357 920 675 835
GAS2L1 73 77 66 32 23 34
RASL10A 9 27 17 0 2 0
AC002059.10 0 0 1 1 1 0
AP1B1 230 272 256 358 244 272
MIR3653 0 0 0 0 0 0
SNORD125 0 0 0 0 0 0
AC000041.8 0 0 0 0 0 0
RFPL4AP6 0 0 0 0 1 0
RFPL1S 116 107 115 6 2 0
AC000041.10 0 0 0 0 0 0
RFPL1 0 0 0 0 0 0
AC000035.3 0 0 0 0 0 0
NEFH 194 265 253 27 24 21
THOC5 73 123 65 218 137 149
CTA-256D12.11 0 0 1 1 2 0
NIPSNAP1 105 131 119 291 188 233
NF2 206 270 235 445 307 342
RPEP4 2 4 1 2 0 3
RP1-76B20.11 0 1 0 0 1 0
RP1-76B20.12 0 0 0 0 0 0
CABP7 18 21 25 2 1 6
ZMAT5 16 12 6 20 20 12
UQCR10 83 94 104 185 98 137
ASCC2 35 42 39 144 91 131
MTMR3 36 46 35 29 15 17
AC004819.1 1 0 1 0 1 0
RNU6-331P 0 0 0 0 0 0
AC003681.1 0 0 1 0 0 0
RP3-394A18.1 81 94 75 86 63 78
MIR6818 0 0 0 0 0 0
HORMAD2-AS1 2 0 0 1 1 0
CNN2P1 0 1 0 0 1 0
HORMAD2 0 0 0 1 5 0
CTA-85E5.7 0 0 0 0 0 0
CTA-85E5.6 0 0 0 0 0 0
RP3-438O4.4 0 0 0 0 2 0
RP1-102K2.6 0 0 0 2 0 0
LIF 2 3 3 154 97 106
RP1-102K2.8 0 0 0 3 1 0
OSM 0 0 1 0 0 2
RP1-102K2.9 2 3 0 0 1 1
GATSL3 5 6 3 2 0 1
RP1-130H16.18 0 0 0 0 0 0
TBC1D10A 13 15 14 39 30 39
SF3A1 184 232 179 388 259 285
CCDC157 3 15 9 9 8 7
RNF215 54 65 42 57 40 47
SEC14L2 53 81 68 42 33 34
RP4-539M6.19 0 0 0 0 0 0
AC004832.1 0 0 1 0 0 0
RP4-539M6.20 3 6 4 4 6 4
RNU6-564P 1 1 0 0 0 0
RP4-539M6.21 0 2 1 4 4 2
MTFP1 0 0 0 3 5 2
RP4-539M6.22 0 0 0 1 1 1
RP4-539M6.18 0 0 0 1 0 0
SEC14L3 1 0 0 0 2 0
RP4-539M6.14 0 0 0 0 0 0
SDC4P 0 0 0 0 0 0
SEC14L4 0 0 0 3 2 4
SEC14L6 4 12 3 3 7 5
SIRPAP1 0 0 0 0 0 0
GAL3ST1 19 18 21 4 6 4
PES1 65 80 70 271 202 255
RP1-56J10.8 0 0 0 0 1 0
TCN2 19 26 23 56 49 40
SLC35E4 18 32 26 21 12 13
DUSP18 8 13 9 12 10 9
CTA-963H5.5 1 2 0 3 0 1
OSBP2 119 137 98 113 57 84
AL022336.1 2 0 0 0 0 0
EIF4HP2 1 4 9 3 6 6
MORC2-AS1 1 2 3 5 2 3
MORC2 75 82 50 146 100 151
TUG1 188 227 207 545 349 397
TUG1_1 0 0 0 0 0 0
TUG1_2 0 0 0 0 0 0
TUG1_3 0 0 0 0 0 0
TUG1_4 0 0 0 0 0 0
RP3-430N8.11 0 0 0 0 0 0
RP3-430N8.10 0 0 0 0 0 0
RP3-412A9.17 0 0 0 2 5 2
RN7SL633P 0 0 0 0 0 0
SMTN 42 51 47 142 91 141
RP3-412A9.16 1 2 2 11 6 4
SELM 83 86 77 25 18 18
RP3-412A9.12 0 0 0 0 0 0
INPP5J 59 77 58 7 8 14
PLA2G3 1 5 2 13 12 8
RP3-412A9.15 0 0 0 0 0 0
MIR3928 0 0 0 0 0 0
RNF185 57 105 74 106 82 90
RNF185-AS1 0 0 0 0 0 0
LIMK2 96 119 103 113 70 95
RNU6-1128P 0 0 0 0 1 0
PIK3IP1 112 165 128 52 32 34
PIK3IP1-AS1 1 1 3 2 0 2
RNA5SP496 0 0 0 0 0 0
PATZ1 72 74 61 191 116 136
LINC01521 12 14 13 8 9 6
RNU6-338P 0 0 0 0 0 0
DRG1 83 105 96 191 143 151
EIF4ENIF1 95 107 96 94 77 78
RP11-247I13.11 0 0 2 1 1 0
RNU6-28P 1 0 0 0 1 1
SFI1 112 125 107 142 102 134
H2AFZP6 1 0 1 0 0 0
RP11-247I13.6 0 0 0 0 0 0
RP11-247I13.3 0 1 1 4 1 4
PISD 195 250 233 156 95 108
MIR7109 0 0 0 0 0 0
PRR14L 219 269 234 418 294 333
DEPDC5 51 79 76 77 50 65
RN7SL20P 0 0 0 1 2 1
CTA-440B3.1 0 0 1 1 2 0
RNU6-201P 0 0 0 0 0 0
RP1-180M12.1 0 1 2 0 0 0
C22orf24 0 6 6 4 2 3
YWHAH 1029 1363 1146 336 220 293
CTA-342B11.1 0 0 0 1 0 0
CTA-342B11.2 0 0 0 0 2 0
RN7SL305P 0 0 0 0 0 0
SC22CB-1E7.1 0 0 0 0 0 0
SLC5A1 0 0 0 0 6 0
AP1B1P1 0 0 0 0 1 0
RP1-127L4.10 0 0 0 0 0 0
AP1B1P2 0 0 0 0 0 0
RP1-127L4.7 0 0 0 1 0 0
C22orf42 0 2 0 0 1 1
RP1-90G24.8 0 0 0 0 0 0
RFPL3-AS1_1 0 0 0 0 0 0
RFPL2 5 3 10 1 1 0
AL008723.1 0 0 0 1 0 0
IGLCOR22-1 0 0 0 0 0 1
RP1-90G24.10 4 7 3 2 3 1
SLC5A4 7 12 5 13 9 4
CPSF1P1 41 43 42 6 12 10
RP1-90G24.6 1 1 3 0 0 0
RP1-90G24.11 0 3 0 1 0 0
RP1-149A16.12 0 1 1 1 0 0
RFPL3 0 0 0 0 0 0
IGLCOR22-2 0 0 0 0 0 0
RFPL3S 1 1 1 0 0 1
RFPL3-AS1_2 0 0 0 0 0 0
RP1-149A16.3 1 3 2 1 1 1
IGLVIVOR22-2 0 0 0 0 0 0
RP1-149A16.17 0 1 0 4 2 0
RP1-149A16.16 2 0 0 2 0 1
RTCB 109 150 124 339 182 249
BPIFC 0 0 0 0 2 0
FBXO7 163 181 194 426 375 371
SYN3 74 110 78 11 12 9
LL22NC03-104C7.1 1 4 5 1 1 1
RNA5SP497 0 0 0 0 0 0
LL22NC01-116C6.1 0 0 1 0 1 0
TIMP3 214 271 243 805 491 604
CTA-415G2.2 0 0 0 0 0 0
RP1-302D9.1 0 0 0 0 0 0
RP1-302D9.2 0 0 0 0 0 1
RP1-302D9.5 0 0 0 0 1 0
LARGE 173 213 199 83 58 84
RP1-302D9.3 0 0 0 0 0 0
SC22CB-1D7.1 1 1 2 3 1 0
MIR4764 1 0 0 0 0 0
SNORA76 0 0 0 0 0 0
SNORA50 0 0 0 0 0 0
LARGE-IT1 0 0 0 0 0 1
LARGE-AS1 7 6 5 5 7 5
LL22NC03-32F9.1 0 0 0 1 0 0
LL22NC03-86D4.1 0 0 0 0 1 0
LL22NC03-13G6.2 0 1 2 0 0 0
RP1-101G11.2 0 0 0 0 0 0
RP1-101G11.3 0 0 0 3 4 2
RP1-288L1.5 2 3 0 0 1 0
RP1-288L1.4 0 0 1 0 0 0
ISX-AS1 1 0 0 2 1 1
ISX 0 0 0 6 4 1
LINC01399 0 0 0 1 0 2
CTA-714B7.7 0 0 0 0 0 0
RP3-323A16.1 0 0 1 75 77 62
CTA-714B7.4 0 0 0 0 0 0
COX7BP1 0 0 0 0 0 0
RNU7-167P 0 0 0 0 0 0
HMGXB4 32 45 49 124 103 102
RP3-510H16.3 2 0 1 0 0 0
TOM1 99 119 103 84 56 68
MIR3909 1 0 0 1 1 0
MIR6069 0 0 0 0 0 0
CTA-286B10.7 0 0 0 1 0 0
CTA-286B10.8 0 0 0 0 0 0
HMOX1 13 19 13 83 51 81
MCM5 29 32 34 544 294 446
RP4-569D19.5 0 0 0 4 1 5
RP4-569D19.8 0 0 0 0 0 0
RASD2 55 81 60 15 15 17
MB 0 1 0 9 8 8
CITF22-62D4.1 0 0 0 0 1 0
APOL6 64 54 56 331 197 254
RP1-41P2.7 0 0 0 0 0 0
MRPS16P3 0 0 0 0 0 0
APOL5 0 0 1 0 0 0
RBFOX2 621 738 711 515 367 405
NDUFA9P1 3 3 2 4 4 3
RP1-78B3.1 10 8 4 21 23 18
CTA-212A2.4 0 0 0 0 0 0
CTA-212A2.3 0 0 0 0 9 0
CTA-212A2.2 0 0 0 0 0 0
CTA-212A2.1 1 0 1 0 1 0
APOL3 8 6 12 39 33 19
Z95114.4 0 0 0 0 1 0
Z95114.3 0 0 0 0 0 0
Z95114.5 0 0 0 0 1 0
Z95114.6 0 0 0 0 1 0
Z95114.7 0 0 0 0 0 0
MTND1P10 0 0 0 0 1 0
APOL4 10 6 8 9 5 4
APOL2 113 151 135 148 112 112
APOL1 4 9 6 87 65 76
MYH9 449 512 485 2685 1608 2111
MIR6819 0 0 0 1 1 0
RP4-633O19__A.1 1 2 1 2 0 0
RPS15AP38 0 0 0 0 1 0
BX470187.1 0 0 0 0 0 0
RP5-1119A7.14 0 1 3 0 0 0
TXN2 27 41 39 82 49 39
FOXRED2 74 108 107 218 104 122
EIF3D 103 119 131 745 494 640
RP5-1119A7.11 0 0 0 0 0 1
RP5-1119A7.10 0 0 0 0 0 0
RP5-1119A7.17 41 56 44 0 0 0
CACNG2 33 34 48 0 1 0
RP1-293L6.1 3 2 4 0 0 0
IFT27 53 58 56 77 57 60
PVALB 100 129 102 25 17 15
CITF22-24E5.1 2 0 0 0 0 0
CTA-833B7.2 0 0 1 1 4 1
NCF4 3 7 1 24 17 15
CSF2RB 2 4 4 50 42 40
CSF2RBP1 0 0 0 0 1 0
LL22NC01-81G9.3 0 0 0 0 1 0
TEX33 0 0 0 0 0 0
TST 18 21 18 88 61 51
MPST 34 29 33 131 76 112
KCTD17 47 74 73 32 21 14
RN7SKP214 0 0 0 1 0 0
TMPRSS6 1 3 0 5 5 3
RP5-1170K4.7 0 0 0 0 1 0
IL2RB 1 0 0 6 6 4
AL022314.1 0 0 0 0 1 0
RP1-151B14.6 0 0 0 1 0 0
C1QTNF6 11 8 10 85 65 67
SSTR3 30 36 48 14 12 12
RP1-151B14.9 0 0 0 0 0 0
RAC2 8 8 5 111 79 92
CYTH4 13 18 16 22 19 12
ELFN2 106 137 114 19 17 23
RP1-63G5.7 1 2 1 1 3 0
RP1-63G5.8 0 0 0 0 0 0
MFNG 4 5 6 75 30 49
CARD10 2 5 5 97 76 74
RP5-1177I5.3 1 1 0 0 0 0
CDC42EP1 68 100 65 144 81 126
LGALS2 0 0 0 7 5 3
GGA1 119 155 128 307 193 221
SH3BP1 20 13 16 55 34 41
Z83844.1 1 3 1 7 2 3
PDXP 5 6 5 2 1 1
RN7SL385P 0 1 0 0 0 0
LGALS1 75 93 78 729 447 618
NOL12 9 10 15 28 17 19
RP1-37E16.12 0 0 0 0 0 0
TRIOBP 36 28 25 164 103 142
H1F0 106 146 112 252 167 190
GCAT 34 27 33 76 56 52
GALR3 1 0 2 1 1 0
ANKRD54 33 48 55 91 50 73
MIR658 0 0 0 0 0 0
MIR659 0 0 0 1 0 0
EIF3L 191 222 206 704 454 597
RP5-1014D13.2 12 23 15 48 32 20
RNU6-900P 0 0 0 0 0 0
MICALL1 52 64 62 149 96 114
RP5-1039K5.12 1 8 1 4 2 1
C22orf23 2 1 5 9 6 5
AL031587.1 0 2 0 0 0 1
RP5-1039K5.19 167 192 150 105 83 72
RP5-1039K5.17 0 0 0 0 0 0
POLR2F 15 28 17 12 8 7
MIR6820 0 0 0 0 0 0
SOX10 0 0 0 0 0 0
MIR4534 0 0 0 0 0 0
RP5-1039K5.16 6 3 10 4 7 0
RP5-1039K5.18 0 0 1 0 1 0
PICK1 79 81 85 46 33 60
RP5-1039K5.13 0 0 0 0 0 0
SLC16A8 9 13 11 11 5 6
BAIAP2L2 5 17 8 18 8 9
CTA-228A9.3 10 3 3 4 2 3
PLA2G6 61 57 62 86 48 50
CTA-228A9.4 2 3 4 13 7 6
MAFF 31 27 20 97 63 68
TMEM184B 207 235 215 191 140 170
RP1-5O6.5 0 0 0 1 0 0
RN7SL704P 0 0 0 0 1 0
AL020993.1 0 0 0 0 0 0
CSNK1E 232 229 222 592 338 447
RP3-449O17.1 10 15 10 30 28 23
RP1-5O6.4 2 0 1 6 4 3
RP3-434P1.6 0 0 0 0 0 0
KCNJ4 49 70 50 2 1 3
KDELR3 6 7 7 106 92 91
DDX17 1532 1797 1637 2814 1818 2243
DMC1 2 4 0 15 11 8
RP1-199H16.6 1 0 0 0 0 0
FAM227A 16 12 17 40 48 22
CBY1 17 19 13 25 22 38
RP3-508I15.10 3 1 0 0 4 2
RP3-508I15.9 12 7 15 7 9 8
TOMM22 52 67 51 178 112 156
JOSD1 149 161 133 261 204 210
GTPBP1 146 187 152 335 182 247
PRDX3P1 3 5 2 11 3 10
RP3-508I15.18 0 0 0 0 2 0
SUN2 289 369 314 266 151 233
RP3-508I15.19 0 2 0 4 1 2
RP3-508I15.20 1 1 1 2 3 3
RP3-508I15.14 1 0 2 3 0 1
RP3-508I15.21 1 5 2 4 9 6
RP3-508I15.22 0 1 1 4 0 2
DNAL4 19 42 34 46 18 27
NPTXR 390 446 394 69 59 50
CBX6 738 873 830 362 240 300
CTA-150C2.13 0 0 0 0 0 0
APOBEC3A 0 0 0 0 1 0
APOBEC3B 1 0 0 19 22 15
APOBEC3B-AS1 0 0 0 0 0 0
APOBEC3C 4 3 3 80 48 59
APOBEC3D 1 1 2 16 8 9
APOBEC3F 1 1 0 11 6 7
APOBEC3G 4 9 3 41 25 22
CTA-150C2.20 0 0 0 0 0 0
RP4-742C19.12 0 2 1 0 0 0
APOBEC3H 4 3 0 0 0 0
CBX7 185 257 208 25 21 24
COX5BP7 0 0 0 0 0 0
RP4-742C19.13 6 19 10 8 6 6
FUNDC2P4 0 0 0 0 0 0
PDGFB 34 45 32 40 28 43
RP3-333H23.8 0 0 0 0 0 1
RPL3 659 761 721 4027 2406 3047
SNORD83B 0 0 0 0 0 0
SNORD83A 2 0 0 7 5 2
AL022326.1 0 0 0 1 1 3
SNORD43 0 0 0 0 0 0
SYNGR1 763 997 870 54 51 42
RP3-333H23.9 1 2 2 0 0 0
TAB1 99 91 70 82 75 86
MGAT3 257 328 274 35 15 24
MGAT3-AS1 5 9 8 1 2 1
MIEF1 95 122 114 312 164 204
ATF4 291 358 307 1354 819 1065
RPS19BP1 72 88 72 129 95 95
CACNA1I 106 139 136 2 7 0
ENTHD1 0 0 0 2 3 3
RP1-172B20.6 0 0 0 0 1 0
RN7SKP210 0 0 0 0 0 0
UQCRFS1P1 1 5 6 4 8 4
GRAP2 1 0 1 64 45 44
RP3-370M22.8 0 0 0 8 1 7
FAM83F 0 1 6 28 20 14
RP3-496C20.1 0 2 0 1 0 2
TNRC6B 582 686 592 528 327 405
RPL7P52 2 4 2 3 2 2
ADSL 40 41 48 302 176 212
RP5-1042K10.14 0 0 1 1 0 0
SGSM3 109 136 114 147 104 131
RP5-1042K10.10 1 2 1 4 4 5
MKL1 139 132 104 137 81 93
RP5-1042K10.13 0 0 1 1 1 3
RP5-1042K10.12 2 0 2 0 4 0
RP4-591N18.2 4 10 8 11 7 9
AL031594.1 1 1 1 2 2 0
COX6B1P3 1 0 0 1 0 0
RPL4P6 1 2 1 8 5 11
GAPDHP37 0 1 0 0 1 0
MCHR1 12 21 17 2 3 2
SLC25A17 39 39 40 119 96 116
RP3-408N23.4 1 1 3 5 1 1
JTBP1 1 1 0 6 1 4
MIR4766 0 0 0 2 0 1
ST13 389 470 463 880 640 760
XPNPEP3 31 43 39 149 105 122
DNAJB7 2 2 0 2 1 0
RNU6-379P 0 0 0 0 0 1
RBX1 50 68 60 122 77 91
AL080243.1 0 0 0 0 0 0
RP11-12M9.3 0 0 0 0 0 0
RP11-12M9.4 0 0 0 0 0 0
EP300 302 403 405 569 328 404
MIR1281 0 0 0 0 0 0
RNU6-375P 0 0 0 0 1 0
RP1-85F18.6 0 3 0 3 3 1
EP300-AS1 1 2 0 1 1 2
LRRC37A14P 0 1 0 0 0 1
L3MBTL2 91 96 83 108 82 88
RP4-756G23.5 6 8 9 2 5 6
CHADL 32 40 39 2 3 1
RANGAP1 256 316 267 464 296 392
MIR6889 0 0 0 0 0 0
ZC3H7B 417 531 475 453 288 372
TEF 335 384 341 43 34 28
RNU6-495P 0 2 0 0 0 0
CTA-223H9.9 0 0 2 4 1 0
TOB2 203 279 197 173 116 145
PHF5A 34 36 17 134 79 89
ACO2 301 366 347 254 168 199
POLR3H 106 93 91 131 77 96
CSDC2 72 94 65 6 5 1
PMM1 34 40 55 51 31 25
DESI1 129 188 159 190 134 135
XRCC6 365 415 378 1431 973 1121
NHP2L1 168 201 178 366 219 291
RNU6-476P 0 1 0 3 1 0
C22orf46 34 36 32 56 46 49
MEI1 1 5 1 8 6 2
HMGN2P10 0 1 0 0 0 0
RNU6ATAC22P 0 0 0 0 0 0
CCDC134 9 24 19 39 24 30
RP5-821D11.7 12 14 13 34 18 23
SREBF2 497 669 575 627 384 539
MIR33A 0 1 2 0 0 0
SHISA8 33 31 18 0 0 4
TNFRSF13C 4 2 2 11 9 12
MIR378I 0 0 0 0 0 0
CENPM 0 3 1 65 35 52
LINC00634 28 16 21 0 1 1
SEPT3 721 907 863 54 38 55
CTA-250D10.19 4 3 4 0 1 0
WBP2NL 14 11 8 5 9 2
SLC25A5P1 0 0 1 0 1 0
NAGA 30 43 53 144 107 132
FAM109B 9 3 4 6 5 6
SNORD13P1 0 0 0 0 1 0
SMDT1 25 42 34 28 15 25
NDUFA6 67 101 81 167 109 126
RP1-257I20.14 2 1 2 8 4 2
NDUFA6-AS1 10 18 21 15 6 11
OLA1P1 1 0 3 3 0 0
CYP2D6 15 23 16 17 9 4
RP4-669P10.19 2 1 0 4 1 5
RP4-669P10.16 1 3 0 2 0 0
RP4-669P10.20 4 6 5 2 2 1
CYP2D7 6 9 8 2 3 10
CYP2D8P 2 3 4 6 7 7
TCF20 205 259 209 455 281 355
OGFRP1 0 3 1 13 6 7
Z83851.4 1 2 1 8 5 5
CTA-989H11.1 1 3 1 8 1 4
LINC01315 1 3 5 2 4 1
NFAM1 5 5 11 8 9 9
CTA-126B4.7 0 0 0 1 1 2
SERHL 4 3 5 2 2 0
RRP7A 59 89 80 157 86 117
Z93241.1 0 0 0 0 0 0
SERHL2 6 11 7 18 14 19
RRP7BP 20 30 18 52 42 45
RN7SKP80 284 319 228 250 413 377
RNU6-513P 0 0 0 0 0 0
POLDIP3 139 155 150 263 169 210
RNU12 6 10 7 17 4 11
CYB5R3 126 169 136 372 250 309
ATP5L2 0 3 1 2 0 0
A4GALT 8 5 2 36 23 25
RPL5P34 0 0 0 0 0 1
GOLGA2P4 0 1 0 0 1 0
RP1-47A17.1 0 0 1 1 2 1
ARFGAP3 53 65 44 187 145 130
PACSIN2 114 127 111 261 174 221
AL049758.2 0 1 0 1 0 0
AL022476.2 5 3 1 0 4 0
TTLL1 16 29 26 10 12 19
AL022237.3 0 1 0 0 0 0
BIK 1 3 6 4 5 6
MCAT 19 27 25 43 27 35
TSPO 12 10 13 136 88 110
TTLL12 57 94 59 278 212 234
SCUBE1 1 5 3 11 15 7
Z82214.3 0 0 0 0 0 0
Z82214.2 0 0 0 0 0 0
Z99756.1 0 0 0 1 0 0
RP4-754E20__A.5 1 0 0 1 3 0
MPPED1 122 154 138 1 3 3
EFCAB6-AS1 2 3 0 0 2 0
EFCAB6 36 43 35 6 4 3
RP3-388M5.8 1 0 1 0 0 1
HMGN2P9 0 0 0 0 0 0
RP3-388M5.9 3 3 6 2 4 5
SULT4A1 290 334 288 5 7 3
PNPLA5 3 2 2 0 3 0
Z97055.1 0 0 0 0 0 0
PNPLA3 6 5 5 45 37 38
SAMM50 45 46 50 132 118 100
RP4-796I17.5 0 1 0 0 0 2
PARVB 69 89 68 162 134 145
CTA-414D7.1 3 6 4 10 10 10
RP4-671O14.6 3 7 5 18 15 8
PARVG 7 10 8 18 19 9
RP4-671O14.5 0 0 1 3 1 0
RP4-671O14.7 0 3 0 3 7 3
KIAA1644 149 205 176 162 111 134
RP1-32I10.10 0 0 0 0 0 0
RP1-32I10.11 0 0 0 0 0 0
CTA-397C4.2 0 0 0 0 0 0
MRPS18CP6 0 0 0 0 0 0
RP5-1033E15.3 0 0 0 0 0 0
LDOC1L 174 261 176 237 149 180
KRT18P23 0 0 0 0 2 0
LINC00207 0 0 0 0 4 0
LINC00229 0 0 0 0 0 0
ANP32BP2 0 0 0 0 0 0
PRR5 10 5 6 26 23 15
PRR5-ARHGAP8 0 1 0 1 1 0
ARHGAP8 2 1 2 6 6 3
PHF21B 15 14 9 16 16 12
RP1-127B20.4 1 1 0 1 1 0
RP4-753M9.1 1 5 0 5 4 2
NUP50-AS1 27 24 31 32 29 28
CTA-217C2.2 1 3 0 6 2 4
NUP50 131 172 154 413 289 319
CTA-268H5.12 0 0 0 0 1 0
KIAA0930 312 364 315 260 166 191
MIR1249 1 2 4 0 1 1
CTA-268H5.14 1 3 1 0 0 0
CTA-268H5.9 0 0 0 0 0 0
UPK3A 0 0 0 2 1 1
FAM118A 53 50 50 113 66 97
SMC1B 3 0 4 6 11 9
RIBC2 0 4 1 12 11 4
RP1-102D24.5 0 0 0 0 1 0
FBLN1 43 47 33 122 96 116
LINC01589 0 0 0 3 1 0
RNU6-1161P 0 0 0 1 0 0
CTA-941F9.10 16 22 15 31 17 29
ATXN10 193 253 246 199 154 170
MIR4762 1 0 0 0 1 1
RP1-37M3.8 0 3 2 5 1 0
WI2-85898F10.2 0 4 3 0 1 0
WI2-85898F10.1 1 0 0 0 0 0
WNT7B 7 11 6 9 9 17
CR536603.1 0 0 0 0 0 0
CITF22-92A6.2 3 2 2 4 5 3
CITF22-92A6.1 0 0 1 1 6 4
LINC00899 7 14 9 7 5 8
PRR34 7 12 15 7 2 3
RP6-109B7.5 4 8 3 0 0 0
PRR34-AS1 6 13 5 15 5 10
MIRLET7BHG 82 137 87 61 56 52
RP6-109B7.2 10 14 11 2 1 6
RP6-109B7.4 17 15 12 6 6 8
MIR3619 2 2 1 5 1 2
MIRLET7A3 0 0 0 0 0 0
MIR4763 0 0 0 0 0 0
MIRLET7B 0 0 0 0 0 0
PPARA 72 101 84 193 147 138
RP4-695O20.1 0 1 1 3 5 4
CDPF1 15 13 11 28 11 19
PKDREJ 6 6 7 8 12 8
TTC38 29 28 20 90 71 85
GTSE1-AS1 2 2 3 2 2 3
GTSE1 2 2 1 145 111 118
TRMU 64 78 75 191 111 140
CELSR1 0 6 4 250 136 195
RP5-996D20.3 0 0 0 0 0 0
RP3-439F8.1 0 0 0 0 9 1
GRAMD4 97 106 75 156 96 135
CERK 209 249 268 298 188 243
CTA-29F11.1 2 6 12 14 13 15
TBC1D22A 39 52 47 78 50 74
U51561.1 1 1 2 1 4 2
FP325331.1 2 4 3 2 1 3
RP1-111J24.1 1 1 0 1 3 0
CITF22-49D8.1 0 1 0 0 2 0
LL22NC03-75H12.2 0 0 0 0 1 0
LINC00898 7 6 1 5 3 1
RP11-191L9.4 8 8 8 32 28 21
RP11-191L9.5 1 0 2 0 2 1
RP13-455A7.1 1 0 0 2 3 0
CTA-280A3.2 4 3 3 7 12 14
CTA-280A3__B.2 0 0 0 0 0 0
LL22NC03-27C5.1 0 0 0 0 2 0
LL22NC03-121E8.4 0 0 0 0 1 0
LL22NC03-121E8.3 0 0 0 0 0 0
MIR3201 0 0 0 0 0 0
RP11-536P6.3 0 0 0 0 0 0
FAM19A5 140 163 151 18 16 14
CTA-299D3.8 17 16 18 0 1 1
MIR4535 0 0 0 0 1 0
AL954742.1 0 0 0 0 0 1
LINC01310 8 7 6 0 9 1
RPL35P8 0 0 0 0 1 0
RP1-34P24.3 0 0 0 0 3 0
C22orf34 2 4 2 36 25 23
CTA-722E9.1 0 0 0 0 3 3
RP4-566L20.1 0 0 0 0 1 5
MIR3667 0 0 0 0 0 0
RP1-29C18.10 0 0 1 13 19 18
RP1-29C18.9 0 0 0 7 1 6
RP1-29C18.8 1 0 1 17 14 8
RP5-983L19.2 0 0 0 0 4 0
RN7SKP252 0 0 0 0 0 0
RPL5P35 0 0 0 0 1 0
BRD1 92 116 103 186 121 160
RP3-522J7.7 3 2 8 5 8 3
RP3-522J7.5 2 3 2 3 3 3
RP3-522J7.6 1 2 1 1 2 0
RP11-494O16.3 0 1 0 0 0 1
RP11-494O16.4 0 0 0 2 0 0
ZBED4 51 68 77 196 153 157
ALG12 21 30 40 53 27 30
CITF22-1A6.3 0 0 0 1 0 1
CRELD2 30 40 43 74 64 57
CITF22-49E9.3 0 0 0 1 4 2
PIM3 47 59 55 159 103 118
MIR6821 0 0 0 0 0 0
IL17REL 0 1 2 0 5 2
TTLL8 0 0 0 0 0 1
MLC1 297 324 307 13 12 12
MOV10L1 10 8 8 0 7 1
RP5-898I4.1 1 0 0 0 1 0
PANX2 59 71 74 9 7 7
TRABD 33 40 37 103 79 87
RP3-402G11.25 2 7 3 4 5 5
RP3-402G11.26 9 17 7 2 0 2
SELO 52 72 33 77 37 65
RP3-402G11.27 7 2 0 5 1 2
RP3-402G11.28 2 2 3 4 2 3
TUBGCP6 248 289 237 279 174 206
HDAC10 4 9 12 9 9 7
MAPK12 60 57 56 116 73 114
MAPK11 64 98 82 25 23 29
PLXNB2 241 301 248 475 285 370
DENND6B 61 101 67 36 20 20
XX-C283C717.1 0 1 0 0 0 0
XX-C00717C00720L.1 0 0 0 0 0 0
PPP6R2 170 249 259 227 150 185
RN7SL500P 0 0 1 0 0 1
SBF1 682 840 696 530 339 422
ADM2 0 2 1 27 21 31
MIOX 0 0 0 1 1 1
LMF2 57 73 69 174 113 164
NCAPH2 86 93 78 219 131 176
SCO2 4 24 10 19 14 22
CTA-384D8.36 8 12 8 7 1 9
TYMP 23 24 30 58 22 33
ODF3B 9 11 9 11 12 11
CTA-384D8.35 0 1 0 0 1 0
CTA-384D8.34 0 0 0 0 0 0
CTA-384D8.31 0 0 0 6 2 0
KLHDC7B 0 0 1 3 8 1
SYCE3 0 0 1 0 0 0
CPT1B 5 3 5 9 8 7
CHKB-CPT1B 2 4 2 6 5 5
CHKB 6 8 4 11 8 4
CHKB-AS1 5 1 3 1 2 1
CTA-384D8.33 0 2 4 1 2 1
MAPK8IP2 410 545 482 13 17 9
ARSA 53 55 65 63 47 53
SHANK3 363 456 375 43 25 35
RNU6-409P 0 0 0 0 0 0
AC000036.4 0 2 1 0 1 0
ACR 0 0 0 0 2 0
AC002056.5 0 0 0 0 0 0
AC002056.3 0 0 0 0 0 0
RPL23AP82 41 59 54 32 23 34
RABL2B 74 62 54 68 50 47
Word, Character, and Line Count in a File
The wc command is used to obtain word, character, and line count in a file.
wc file.txt
The output (from left to right) for wc can be interpreted as follows.
- 2 indicates that the file has two lines.
- 23 indicates that the file has 23 words.
- 135 indicates that the file has 135 characters.
- The file in which statistics were generated (ie. file.txt).
2 23 135 file.txt
The wc results above can be obtained separately. For instance, to just get the number of lines in a file include the -l option.
wc -l file.txt
2 file.txt
Word count can be obtained using the -w option.
wc -w file.txt
23 file.txt
Character count can be obtained uisng the -m option.
wc -m file.txt
135 file.txt
Pattern Searching
Sometimes users may want to search for a keyword in a file. The grep command can be used to do this. The grep command prints every line in a file that contains the search pattern. The arguments in grep are as follows.
- Search pattern (ie. Linux)
- File to search (ie. file.txt)
grep Linux file.txt
Linux is a variety of Unix, and sometimes the names are used interchangeably.
To search for lines that do not contain a pattern include the -v option.
grep -v Linux file.txt
Unix is an operating system, just like Windows or MacOS.
What would happen if "linux" with a lower case "l" is used as the search pattern instead of an upper case "L" as shown in the file.txt? Nothing is returned because grep is case sensitive. To ignore case, include the -i option.
grep linux file.txt
grep -i linux file.txt
Linux is a variety of Unix, and sometimes the names are used interchangeably.
Working with Software Installed on Biowulf
The module command is important for anyone who wishe to work with software that are installed on Biowulf. This avail option enables users to browse the software that are available on the cluster.
module avail
Glimpse of module avail results. Users can scroll up/down using the arrow keys to learn what software are available. Hit Q to exit the module avail results and return to the prompt.
----------------------------------------------------- Global Aliases -----------------------------------------------------
bowtie1 -> bowtie/1.3.1 deeptrio/1.6.0 -> deepvariant/1.6.0-deeptrio
bowtie2 -> bowtie/2-2.5.3 deeptrio/1.6.1 -> deepvariant/1.6.1-deeptrio
deeptrio/1.5.0 -> deepvariant/1.5.0-deeptrio
-------------------------------------------- /data/classes/BTEP/apps/modules ---------------------------------------------
biostars/1.0
---------------------------------------------- /usr/local/lmod/modulefiles -----------------------------------------------
3DSlicer/4.8.1 hwloc/2.9.3/gcc-8.5.0
3DSlicer/5.2.2 (D) hwloc/2.9.3/gcc-9.2.0
To find if a particular software is available include the software name with the avail option.
module avail fastqc
----------------------------------------------------- Global Aliases -----------------------------------------------------
---------------------------------------------- /usr/local/lmod/modulefiles -----------------------------------------------
fastqc/0.11.8 fastqc/0.11.9 fastqc/0.12.1 (D)
Where:
D: Default Module
Module defaults are chosen based on Find First Rules due to Name/Version/Version modules found in the module tree.
See https://lmod.readthedocs.io/en/latest/060_locating.html for details.
If the avail list is too long consider trying:
"module --default avail" or "ml -d av" to just list the default modules.
"module overview" or "ml ov" to display the number of modules for each name.
Use "module spider" to find all possible modules and extensions.
Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".
To get a description of a software use module whatis.
module whatis fastqc
fastqc/0.12.1 : fastqc: It provide quality control functions to next gen sequencing data.
fastqc/0.12.1 : Version: 0.12.1
Warning
Upon signing onto Biowulf, users will land in the "log-in" node, which is not meant for analyzing data or transferring files. To perform these task, request time and resources on a compute node using the sinteractive command. To learn more about the sinteractive command, see https://bioinformatics.ccr.cancer.gov/docs/unix-on-biowulf-2024/Lesson4/#requesting-an-interactive-session
To load a software use module load followed by the name of the package.
module load samtools
[+] Loading samtools 1.19 ...
Getting Help
To get help, use the man command which pulls up the manual for a command. Use the up and down arrow keys to scroll through the manual and learn about the different options. Hit q to return to exit man and return to the prompt.
For instance, to pull up the manual for grep, do the following.
man grep
Glimpse of man command output for grep.
GREP(1) General Commands Manual GREP(1)
NAME
grep, egrep, fgrep - print lines matching a pattern
SYNOPSIS
grep [OPTIONS] PATTERN [FILE...]
grep [OPTIONS] -e PATTERN ... [FILE...]
grep [OPTIONS] -f FILE ... [FILE...]
DESCRIPTION
grep searches for PATTERN in each FILE. A FILE of “-” stands for standard input. If no
FILE is given, recursive searches examine the working directory, and nonrecursive
searches read standard input. By default, grep prints the matching lines.
In addition, the variant programs egrep and fgrep are the same as grep -E and grep -F,
respectively. These variants are deprecated, but are provided for backward
compatibility.
OPTIONS
Generic Program Information
--help Output a usage message and exit.
-V, --version
Output the version number of grep and exit.
Continual Learning
- See https://bioinformatics.ccr.cancer.gov/docs/unix-on-biowulf-2024/ for a more detailed Unix and Biowulf class. Check the BTEP Calendar for upcoming advanced Unix classes. Email ncibtep@nih.gov or drop by BTEP's Virtual Office Hours with questions.
- Coursera and Dataquest offers self learning classes for Unix and other data science related topics such as R and Python programming. See https://bioinformatics.ccr.cancer.gov/btep/self-learning/ to learn how to request a Coursera or Dataquest license.
- Example Coursera classes:
- Example Dataquest classes: