BTEP maintains several Question and Answer Forums of interest to the NCI/CCR community.
Currently, there are forums on these topics listed below:
If you wish to ask a question go to the Ask Question Page and submit your question.
July 2nd, 2024
STATA file backups
Categories: Statistics
Views: 587 Asked By: caroline.pruitt@nih.govHello! I\'m using STATA18 and every time I save a DO file, the next time I go to open the file I get a pop-up asking if I want to use the recovered version. It also looks like temporary files are being saved. I\'ve tried doing both \"Save\" and \"Save As\" to replace older versions of the file but I\'m concerned there\'s an issue in the way that I\'m saving things
November 28th, 2023
Statistics Help
Categories: FAQ, General
Views: 733 Asked By: john.hancock@nih.govWho should I contact regarding statistics help and guidance beyond training?
April 4th, 2023
Exporting plots with R
Categories: R
Views: 813 Asked By:April 4th, 2023
Labeling select data points on a plot
Categories: R
Views: 912 Asked By:April 4th, 2023
Practicing R with DNAnexus
Categories: R
Views: 776 Asked By:April 4th, 2023
Help with R syntax
Categories: R
Views: 838 Asked By:April 4th, 2023
BTEP R course help sessions
Categories: R
Views: 774 Asked By:April 4th, 2023
BTEP R Courses
Categories: R
Views: 780 Asked By:April 4th, 2023
Data visualization example code
Categories: R
Views: 789 Asked By:April 2nd, 2021
Unix Quiz 1
Views: 5072 Asked By:March 31st, 2021
Elizabeth Introduction
Views: 5110 Asked By:March 31st, 2021
Joanne Introduction
Views: 4913 Asked By:March 31st, 2021
Ryan Introduction
Views: 5018 Asked By:March 30th, 2021
Can we have a brief introduction of types of data in Bioinformatics?
Views: 4884 Asked By:March 30th, 2021
Introduction
Views: 5038 Asked By:Hi everyone! My name is Mythili Merchant and I am a postbac in Dr. Jing Wu's lab at the Neuro-Oncology Branch in Bethesda! My projects are mainly focused on understanding the landscape of gliomas and development of therapeutics.
I have enjoyed bioinformatics for a long time, but have always focused on using GUI for database mining mainly to characterize functions of hypothetical genes. However, I have been hoping to learn more about working with NGS data and to learn how to analyze and use it. Also, hoping to pick up some other useful skills along the way!
Looking forward to getting to know everyone! See you all on Thursday at 3 pm.
March 30th, 2021
Introduction - Corey Young
Views: 5265 Asked By:March 30th, 2021
Will we cover R/Python for bioinformatics in this course?
Views: 5795 Asked By:March 30th, 2021
Introduction
Views: 5472 Asked By:March 30th, 2021
how can i get help in this class?
Views: 5118 Asked By:March 30th, 2021
Analyzing Short/Long read sequencing results and interpreting splicing events.
Views: 5531 Asked By:February 23rd, 2021
Trouble building CTAT custom genome
Views: 5444 Asked By:July 30th, 2020
Why don’t the scRNA transcript counts match up with the results I found with flow cytometry?
Categories: Single-Cell RNA-Seq
Views: 5812 Asked By:July 29th, 2020
Do I need to have extensive bioinformatic knowledge to explore my Cell Ranger results?
Categories: Single-Cell RNA-Seq
Views: 5449 Asked By:July 29th, 2020
What is Cell Ranger?
Categories: Single-Cell RNA-Seq
Views: 5498 Asked By:July 29th, 2020
For single nuclei RNA-Seq, do I have to do anything different in handling the data?
Categories: Single-Cell RNA-Seq
Views: 5348 Asked By:July 25th, 2020
Can you say something about trajectory analysis vs. velocity analysis?
Categories: Single-Cell RNA-Seq
Views: 12635 Asked By:July 25th, 2020
Can you give some suggestions cell identity annoation and recommend packages good at cell identity annotation? What is the most used practice, manually or auto?
Categories: Single-Cell RNA-Seq
Views: 6646 Asked By:July 23rd, 2020
How can I use a large data set like Tabula Muris for identifying cell types in my data?
Categories: Single-Cell RNA-Seq
Views: 6323 Asked By:July 18th, 2020
What sequencing depth do I need for scRNA-Seq samples?
Categories: Single-Cell RNA-Seq
Views: 7232 Asked By:July 18th, 2020
When should we batch correct scRNA-Seq data? When should we avoid it?
Categories: Single-Cell RNA-Seq
Views: 19651 Asked By:July 18th, 2020
Droplet-based (e.g. 10x Genomics) or plated-based (e.g. Smart-Seq)? When should one be considered over the other
Categories: Single-Cell RNA-Seq
Views: 9755 Asked By:July 18th, 2020
Difference between 3' and 5' gene expression profiling? Which should I use?
Categories: Single-Cell RNA-Seq
Views: 14813 Asked By:July 17th, 2020
questions related to single cell ATAC-seq?
Categories: Single-Cell RNA-Seq
Views: 3204 Asked By:July 17th, 2020
a few experimental design-related questions on single cell RNA-seq?
Categories: Single-Cell RNA-Seq
Views: 3485 Asked By:- We are planning to multiplex ~8 solid tissue samples (normal human lung) for scRNA-seq using natural barcodes and we have a few experimental design-related questions.
- The main optimization we need is to keep the integrity of all the cell types in the tissue throughout fresh tissue dissociation-freezing-thawing-multiplexing procedure. We are concerned that epithelial cell types (the type that we are most interested in) are especially vulnerable to freeze-thawing process. What would you recommend to optimize to achieve this goal? For example, we are looking into adjusting the enzyme content/concentration to make the dissociation step less harsh to epithelial populations, as well as testing different freezing media.
- To achieve the cell viability of cryopreserved cells suitable for 10X 3’ sequencing, would it be worth comparing commercial dead cell removal kit vs. FACS sorting directly into 10X library for removing dead cells after thawing?
- What considerations should go into pilot testing for an efficient way to process 8 samples at the same time to minimize cell loss during the potentially long hands-on time?
- We are aiming to multiplex 8 samples based on the feasibility stated in the literature, but do you have experience on how feasible it is in reality? E.g. should we consider testing 4 samples to maximize the success in sample identify deconvolution?
- We are planning of a pilot experiment of 10X 3’ RNA for a couple of 8-plexed reaction before we expand onto larger samples. In addition to the standard QC metrics (e.g. viability, number of detected cells and genes per cell, mitochondrial content etc) what would you recommend to pay attention to to determine the quality of the data?
- In general, validity of cell clusters based on the gene expression might be hard to assess. What are the methods that you recommend to validate the quality of our final results? (e.g. mapping to public clustering data of the same tissue type, matching to Flow cytometry data for select markers, CITE-seq for a limited antibody profile)
July 16th, 2020
How many cells can I capture in my experiment?
Categories: Single-Cell RNA-Seq
Views: 2673 Asked By:July 16th, 2020
Which cell types can be used in Single-Cell RNA Seq?
Categories: Single-Cell RNA-Seq
Views: 2205 Asked By:June 17th, 2020
Local vs. global alignment
Categories: BIOSTAR
Views: 6557 Asked By:June 5th, 2020
Should we always use histone markers just to see if our sequencing is working for our samples?
Categories: ChIP-Seq Data Analysis
Views: 2735 Asked By:June 5th, 2020
What do you think about ChIP-seq with proteins that are highly mobile in nature? Why is there less data published about using them?
Categories: ChIP-Seq Data Analysis
Views: 2669 Asked By:June 5th, 2020
I had great results with ChIP-qPCR, but when I did ChIP-seq only a few reactions came up with decent peaks. What could be the reason?
Categories: ChIP-Seq Data Analysis
Views: 2703 Asked By:June 5th, 2020
Comparing to outside sources of data: What is a good website to check for transcription factor binding motifs and how they regulate expression?
Categories: ChIP-Seq Data Analysis
Views: 2636 Asked By:What is a good website to check for transcription factor binding motifs and how they regulate expression?
June 5th, 2020
Comparing to outside sources of data: Do you have recommendations for frameworks or programs for integrating ChIP-seq and RNA-seq or microarray data?
Categories: ChIP-Seq Data Analysis
Views: 2583 Asked By:June 5th, 2020
Replicates: Can you talk a little bit about IDR? Is IDR something you must do for transcription factor ChiP-seq or is it optional?> What about with histone marks? Does IDR work with MACS2 outputs?
Categories: ChIP-Seq Data Analysis
Views: 3558 Asked By:June 5th, 2020
Replicates: If my replicates are highly reproducible, is it valid to merge my replicates before finding peaks?
Categories: ChIP-Seq Data Analysis
Views: 3593 Asked By:June 5th, 2020
Peak calling and analyses: What do you think about ChIPseeker for annotation?
Categories: ChIP-Seq Data Analysis
Views: 3023 Asked By:June 5th, 2020
Peak calling and analyses: When I call peaks with MACS2, can I use one ChIP (antibody1) as the control for a second ChIP antibody? Can I detect differences between the two proteins that way?
Categories: ChIP-Seq Data Analysis
Views: 3584 Asked By:When I call peaks with MACS2, can I use one ChIP (antibody1) as the control for a second ChIP antibody? Can I detect differences between the two proteins that way?
June 5th, 2020
Peak calling and analyses: If the control is input, which method peak calling do you prefer?
Categories: ChIP-Seq Data Analysis
Views: 2729 Asked By:June 5th, 2020
Peak calling and analyses: What peak caller is good for broad peaks?
Categories: ChIP-Seq Data Analysis
Views: 2815 Asked By:June 5th, 2020
Pipelines and QC:What package do you use to perform a partial duplicate removal?
Categories: ChIP-Seq Data Analysis
Views: 2716 Asked By:June 5th, 2020
Pipelines and QC: Does the mouse genome have a blacklist file?
Categories: ChIP-Seq Data Analysis
Views: 2859 Asked By:June 5th, 2020
Pipelines and QC: When and how do you remove blacklisted regions? What program do you use?
Categories: ChIP-Seq Data Analysis
Views: 4410 Asked By:June 5th, 2020
Pipelines and QC: What is "effective genome size"?
Categories: ChIP-Seq Data Analysis
Views: 3095 Asked By:June 5th, 2020
Pipelines and QC: Since reads are mapped to unique regions of the genome, what happens with data from repeat regions such as long non-coding RNA, LINEs, etc? Will any reads be mapped to these regions?
Categories: ChIP-Seq Data Analysis
Views: 1491 Asked By:June 5th, 2020
Pipelines and QC: What are "no hits" on a multiQC report? Are they all adaptors?
Categories: ChIP-Seq Data Analysis
Views: 1624 Asked By:June 5th, 2020
Pipelines and QC: What is the average length of a read produced by ChIP-seq?
Categories: ChIP-Seq Data Analysis
Views: 1581 Asked By:June 5th, 2020
Pipelines and QC: What is a good mapping percentage?
Categories: ChIP-Seq Data Analysis
Views: 1608 Asked By:June 5th, 2020
Pipelines and QC: Which ChIP-seq pipelines mentioned in your talk can handle paired-end reads?
Categories: ChIP-Seq Data Analysis
Views: 1522 Asked By:June 5th, 2020
ChIP-seq versus other sequencing methods: What is CUT & RUN? How do you compare ChIP-seq and CUT & RUN?
Categories: ChIP-Seq Data Analysis
Views: 4503 Asked By:June 5th, 2020
ChIP-seq versus other sequencing methods: What are the advantages and disadvantages of using ChIP-seq instead of ATAC-seq?
Categories: ChIP-Seq Data Analysis
Views: 3705 Asked By:June 5th, 2020
Spike-ins: At what stage of the ChIP experiment do you introduce the spike-ins?
Categories: ChIP-Seq Data Analysis
Views: 1504 Asked By:June 5th, 2020
Spike-ins: Can you please give me more detail on how the spike-in works?
Categories: ChIP-Seq Data Analysis
Views: 1829 Asked By:June 5th, 2020
Spike-ins: How much spike-in is a good amount to use?
Categories: ChIP-Seq Data Analysis
Views: 1613 Asked By:How much spike-in is a good amount to use?
June 5th, 2020
Spike-ins: What is a good spike-in sample for ChIP-seq?
Categories: ChIP-Seq Data Analysis
Views: 1782 Asked By:June 5th, 2020
Genetic Variants and ChIP-seq data: When we are working with patient samples for ChIP-seq, we align them all to one generic reference genome. Will the alignment tolerate and SNPs in the individual patient line?
Categories: ChIP-Seq Data Analysis
Views: 1391 Asked By:When we are working with patient samples for ChIP-seq, we align them all to one generic reference genome. Will the alignment tolerate any SNPs in the individual patient line?
June 5th, 2020
Genetic Variants and ChiP-seq data: Can you use ChIP-seq data to analyze copy number variants? Can you do structural. variant calling?
Categories: ChIP-Seq Data Analysis
Views: 1605 Asked By:June 5th, 2020
Library ChIP preparation: How do I choose between sonication and enzymatic-based chromatin fragmentation for ChIP-seq? How might this affect sequencing depth?
Categories: ChIP-Seq Data Analysis
Views: 1855 Asked By:How do I choose between sonication and enzymatic-based chromatin fragmentation for ChIP-seq? How might this affect sequencing depth?
June 5th, 2020
Library ChiP preparation: Is the sequencing depth based on the organism you're working with?
Categories: ChIP-Seq Data Analysis
Views: 1506 Asked By:June 5th, 2020
Library ChIP preparation: What happens if there are too many PCR cycles?
Categories: ChIP-Seq Data Analysis
Views: 1620 Asked By:June 5th, 2020
Library ChIP preparation: What should be the starting amount of DNA for fresh and fixed sample?
Categories: ChIP-Seq Data Analysis
Views: 1492 Asked By:June 5th, 2020
Library ChIP preparation: Can ChIP-seq be done on formalin fixed tissue and if yes how much starting material is usually required?
Categories: ChIP-Seq Data Analysis
Views: 1529 Asked By:June 5th, 2020
Library/ChIP preparation: Is it okay to use frozen samples or is it better to use fresh cells?
Categories: ChIP-Seq Data Analysis
Views: 1740 Asked By:June 5th, 2020
Library/ChIP preparation: What if my antibody has low binding affinity and there isn't a better option available?
Categories: ChIP-Seq Data Analysis
Views: 1484 Asked By:June 5th, 2020
Library/ChIP preparation: What are nanobodies? Can they be used for ChIP-Seq?
Categories: ChIP-Seq Data Analysis
Views: 2801 Asked By:What are nanobodies? Can they be used for ChIP-Seq?
June 5th, 2020
Control Types: Is there a bias with ChIP-Seq data because promoters tend to be GC-rich and tend to be open chromatin regions?
Categories: ChIP-Seq Data Analysis
Views: 1477 Asked By:Is there a bias with ChIP-Seq data because promoters tend to be GC-rich and tend to be open chromatin regions?
June 5th, 2020
Control Types: Is it ever useful to do a non-specific antibody first, then a specific antibody?
Categories: ChIP-Seq Data Analysis
Views: 2276 Asked By:June 5th, 2020
Control Types: Why does my IgG control sample have higher binding than the antibody binding sample for qPCR? What do I do about it?
Categories: ChIP-Seq Data Analysis
Views: 2064 Asked By:June 5th, 2020
Control Types: Is there a reason not to use both IgG and Input controls?
Categories: ChIP-Seq Data Analysis
Views: 1532 Asked By:June 5th, 2020
Control Types: Under what conditions is it better to use the Input versus IgG control for ChIP-Seq?
Categories: ChIP-Seq Data Analysis
Views: 3286 Asked By:June 5th, 2020
Control Types: What is copy number bias? How are we supposed to address it for ChIP-Seq?
Categories: ChIP-Seq Data Analysis
Views: 1412 Asked By:June 5th, 2020
Control Types: What is the difference between input and naked DNA?
Categories: ChIP-Seq Data Analysis
Views: 1851 Asked By:What is the difference between in put and naked DNA?
June 4th, 2020
Issues with installing jellyfish on a MAC computer
Categories: BIOSTAR
Views: 2743 Asked By:I am trying to install jellyfish on my Mac computer. Typing "make install" gives me an error like:
/usr/local/lib/libjellyfish-2.0.2.dylib: Permission denied
or
mkdir: /usr/local/lib: Permission denied
May 28th, 2020
Control Types: Can we use any DNA-seq as an input sample?
Categories: ChIP-Seq Data Analysis
Views: 1783 Asked By:Can we use any DNA-seq as an input sample?
May 21st, 2020
Lecture recording and notes
Categories: BIOSTAR
Views: 2568 Asked By:Are our lectures/classes recorded, and if so where can we access them?
May 13th, 2020
Error using parallel tool for fast-dump
Categories: BIOSTAR
Views: 2789 Asked By:cat runids.txt | parallel fastq-dump -X 10000 --split-filesMay 13th, 2020
CSVKit issue in biowulf
Categories: BIOSTAR
Views: 2689 Asked By:May 10th, 2020
How to quickly activate bioinfo in biowulf?
Categories: BIOSTAR
Views: 2593 Asked By:[user@biowulf temp]$ source /data/$USER/conda/etc/profile.d/conda.sh [user@biowulf temp]$ conda activate bioinfo
I tried both creating a bioinfo.sh shell script and defining an alias called bioinfo to
quickly activate bioinfo, but all failed. Could you please help me with that? Thanks
April 30th, 2020
what does -f stand for in the bash profile setup?
Categories: BIOSTAR
Views: 4407 Asked By:# if [ -f ~/.bashrc ]; then source ~/.bashrc fi
April 27th, 2020
What are the Rules and Purpose of this Forum
Views: 2440 Asked By:April 24th, 2020
Error in library(DESeq)
Categories: BIOSTAR
Views: 3778 Asked By:I am running the command line shown in chapter XXII (cat simple_counts.txt | Rscript deseq1.r 3x3 > result.txt)
This returned an error message "dyld: Library not loaded: @rpath/libreadline.6.2.dylib
Referenced from: /Users/yangc2/miniconda3/envs/bioinfo/lib/R/lib/libR.dylib
Reason: image not found
Abort trap: 6".
I also tried the other Rscripts deseq2.r and edger.r. But all gave a similar error message and no correct output file. Is there a way to resolve this?
I am running this in Ubuntu/PC.
=============================================
Kudos to Amy's feedback. It turned out to be some setting issue with the r software package. This issue is resolved by re-running the codes as follow:
conda install r
conda install -y bioconductor-deseq bioconductor-deseq2 bioconductor-edger r-gplotsApril 23rd, 2020
how to use commend lines to do data analysis?
Categories: BIOSTAR
Views: 2360 Asked By:- I just copy from biostar and paste them into terminal and ran well with those commends according to biostar book But I still do not know how to do them by myself. Do you guys have any good suggestions about what I should do to learn the knowledge from the book to use for my own use? instead of copy and paste from biostar website?
- Could you help to demonstrate how to do data analysis with unix commend lines in terminal in the class, instead of just follow the book to copy and paste the commends lines into terminal? That will be more helpful and help us to learn how to use the commend to solve the problems.
April 23rd, 2020
How to do the exercise from the book with Chr22 and hg38 but with hg37
Categories: BIOSTAR
Views: 2653 Asked By:I typed this command
$ curl https://hgdownload.soe.ucsc.edu/goldenPath/hg19/chromosomes/chr22.fa.gz | gunzip -c > ~/refs/hg37/chr22.fa
But It just show up the next
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
April 22nd, 2020
Can you recover a removed file after issuing the rm command?
Categories: BIOSTAR
Views: 2635 Asked By:Can you recover a removed file after issuing the rm command?
April 22nd, 2020
How to enable colors for the ls command
Categories: BIOSTAR
Views: 1737 Asked By:April 22nd, 2020
Customizing your terminal prompt?
Categories: BIOSTAR
Views: 2482 Asked By:April 21st, 2020
efetch, bgzip, infoseq, seqkit, bioawk – commands not found. Do I need to install something?
Categories: BIOSTAR
Views: 3698 Asked By:Update: found the problem - I had not activated bioinfo in the new terminal window! Its all working now. :)
Leaving this question here in case anybody else is facing the same issue.
Original question - Most of the commands described in the data compression and subsequent chapters are not working - On trying commands like efetch, bgzip, infoseq, seqkit, bioawk etc, I get 'command not found'. Is there any additional the needs to be installed for these?
April 20th, 2020
Asking before deleting
Categories: BIOSTAR
Views: 1616 Asked By:Hi, during the last session the instructor showed that her Terminal would confirm before deleting a directory or file. I thought the instructions for how to set up our environment to do the same were going to be posted here.
Thanks for your help
Diana
April 16th, 2020
Makefile target command problems
Categories: BIOSTAR
Views: 1904 Asked By:April 14th, 2020
trouble installing makefiles
Categories: BIOSTAR
Views: 2449 Asked By:I used conda install make, but the condo install makefiles does not work. I get this error:
$ conda install Makefiles
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
PackagesNotFoundError: The following packages are not available from current channels:
- makefiles
Current channels:
- https://conda.anaconda.org/bioconda/osx-64
- https://conda.anaconda.org/bioconda/noarch
- https://conda.anaconda.org/conda-forge/osx-64
- https://conda.anaconda.org/conda-forge/noarch
- https://repo.anaconda.com/pkgs/main/osx-64
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/r/osx-64
- https://repo.anaconda.com/pkgs/r/noarch
To search for alternate channels that may provide the conda package you're
looking for, navigate to
https://anaconda.org
and use the search bar at the top of the page.
(bioinfo)
April 12th, 2020
Ubuntu on Windows installation issues
Categories: BIOSTAR
Views: 2528 Asked By:April 9th, 2020
How to install Ubuntu if you are located at NCI Frederick
Categories: BIOSTAR
Views: 1645 Asked By:April 9th, 2020
Ubuntu Linux on Windows link
Categories: BIOSTAR
Views: 1925 Asked By:April 9th, 2020
The miniconda download does not work!
Categories: BIOSTAR
Views: 2128 Asked By:It does not download, I just get an error message.
April 9th, 2020
More trouble with Xcode
Categories: BIOSTAR
Views: 1962 Asked By:April 7th, 2020
Administrator issues with PC government computer
Categories: BIOSTAR
Views: 2754 Asked By:How will I be able to install the programs on the PC government computer?
April 6th, 2020
MacOS users: Where to find older versions of XCode?
Categories: BIOSTAR
Views: 25721 Asked By:In going through the macOS computer setup instructions in the biostar handbook, the XCode version in the App Store requires macOS version 10.15.2 or later. What if I am using an older version of the macOS?
April 2nd, 2020
Which shell to use for Mac OS Catalina (10.15.*)
Categories: BIOSTAR
Views: 2126 Asked By:April 2nd, 2020
What are the Rules and Purpose of this Forum
Categories: BIOSTAR
Views: 5814 Asked By:April 2nd, 2020
What is the difference between RPKM, FPKM and TPM
Categories: FAQ
Views: 89532 Asked By: