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Lesson 2

Lesson 2 practice

For these practice questions, check the present working directory and if needed, change into the /data/username folder (username is the student account ID).

What command is used to check present working directory?

Solution

pwd

If not in the /data/username folder, then what is the approach to change into it?

Solution

cd /data/username

Copy the lesson_2_practice folder from /data/classes/BTEP/unix_on_biowulf_2023_practice_sessions to the present working directory, which should be /data/username folder.

Solution

cp -r /data/classes/BTEP/unix_on_biowulf_2023_practice_sessions/lesson2_practice .

Change into lesson2_practice.

Solution

cd lesson2_practice

How many files and how many directories are in lesson2_practice?

Solution

There are four files and no directories.

ls -l

-rw-r----- 1 wuz8 wuz8 19336 May 11 16:34 nc_002549_1.fasta
-rw-r----- 1 wuz8 wuz8 30429 May 11 16:34 nc_0045512_2.fasta
-rw-r----- 1 wuz8 wuz8  1468 May 11 16:34 OK572970_1.fasta
-rw-r----- 1 wuz8 wuz8   265 May 11 16:34 OQ946980_1.fasta

Take a look at OQ946980_1.fasta, what organism did this sequence come from?

Solution

cat OQ946980_1.fasta

>OQ946980.1 Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/Chiroptera/MYS/S4/2021 ORF10 protein (ORF10) gene, partial cds
TCTACTCTTGCGCAGAATGAATTCTCGTAACTACATAGCACAAGTAGATGTAGTTAACTTTAATCTCACA
TAGCAATCTTTAATCAGTGTGTAACATTAGGGAGGACGTGAAAGAACCAC

Change back to /data/username. Again, replace username with the student account ID.

Download the fastq files from http://genomedata.org/rnaseq-tutorial/HBR_UHR_ERCC_ds_5pc.tar. Save the output as HBR_UHR_ERCC_ds_5pc.tar.

Solution

curl -o HBR_UHR_ERCC_ds_5pc.tar http://genomedata.org/rnaseq-tutorial/HBR_UHR_ERCC_ds_5pc.tar

Unpack HBR_UHR_ERCC_ds_5pc.tar, how many fastq files are there?

Solution

tar -xvf HBR_UHR_ERCC_ds_5pc.tar

There are 12 fastq files.

HBR_Rep1_ERCC-Mix2_Build37-ErccTranscripts-chr22.read1.fastq.gz
HBR_Rep1_ERCC-Mix2_Build37-ErccTranscripts-chr22.read2.fastq.gz
HBR_Rep2_ERCC-Mix2_Build37-ErccTranscripts-chr22.read1.fastq.gz
HBR_Rep2_ERCC-Mix2_Build37-ErccTranscripts-chr22.read2.fastq.gz
HBR_Rep3_ERCC-Mix2_Build37-ErccTranscripts-chr22.read1.fastq.gz
HBR_Rep3_ERCC-Mix2_Build37-ErccTranscripts-chr22.read2.fastq.gz
UHR_Rep1_ERCC-Mix1_Build37-ErccTranscripts-chr22.read1.fastq.gz
UHR_Rep1_ERCC-Mix1_Build37-ErccTranscripts-chr22.read2.fastq.gz
UHR_Rep2_ERCC-Mix1_Build37-ErccTranscripts-chr22.read1.fastq.gz
UHR_Rep2_ERCC-Mix1_Build37-ErccTranscripts-chr22.read2.fastq.gz
UHR_Rep3_ERCC-Mix1_Build37-ErccTranscripts-chr22.read1.fastq.gz
UHR_Rep3_ERCC-Mix1_Build37-ErccTranscripts-chr22.read2.fastq.gz