ncibtep@nih.gov

Bioinformatics Training and Education Program

BTEP Question Forum

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.


November 28th, 2023

Statistics Help

Categories: FAQ, General

Tags: Statistics

Views: 146   Asked By: john.hancock@nih.gov

Who should I contact regarding statistics help and guidance beyond training?

   View 1 Answer

April 4th, 2023

Exporting plots with R

Categories: R

Tags: data visualization

Views: 263   Asked By:
What are the ideal dimensions and recommendations for exporting visuals?
   View 1 Answer

April 4th, 2023

Labeling select data points on a plot

Categories: R

Tags: data visualization

Views: 292   Asked By:
If I want to label one data point in a PCA or volcano plot, how would I go about doing that?
   View 1 Answer

April 4th, 2023

Practicing R with DNAnexus

Categories: R

Views: 242   Asked By:
How can I use DNAnexus outside of BTEP classes to practice R?
   View 1 Answer

April 4th, 2023

Help with R syntax

Categories: R

Views: 249   Asked By:
Where can we get more help on the R syntax?
   View 1 Answer

April 4th, 2023

BTEP R course help sessions

Categories: R

Views: 236   Asked By:
Can we attend BTEP R course help sessions to seek help for R projects / questions unrelated to the current lesson?
   View 1 Answer

April 4th, 2023

BTEP R Courses

Categories: R

Tags: data science

Views: 253   Asked By:
Will we get the opportunity to work with our own data in BTEP R courses?
   View 1 Answer

April 4th, 2023

Data visualization example code

Categories: R

Tags: data visualization

Views: 249   Asked By:
Where can I find examples of different types of plots made using R?
   View 1 Answer

April 2nd, 2021

Unix Quiz 1

Views: 4528   Asked By:
Hi, Could you explain more why .jarjarbinks is a valid file extension? Thank you!
   View 1 Answer

March 31st, 2021

Elizabeth Introduction

Views: 4546   Asked By:
Hello, my name is Elizabeth and I'm a postbac in Dr. Dinah Singer's lab. My project focuses on understanding additional functions of a transcription factor, including RNA binding. I'm interested in better understanding the methods used to analyze genomic and sequencing data.
   View 1 Answer

March 31st, 2021

Joanne Introduction

Views: 4367   Asked By:
Hello! My name is Joanne Unite and I am a post-bac in Dr. Lewandoski's lab within the CDBL at NCI-Fredrick. Our lab studies gene gain/loss of function in mouse embryonic development. I am taking this class to get experience in bioinformatics techniques. 
   View 1 Answer

March 31st, 2021

Ryan Introduction

Tags: Introduction

Views: 4486   Asked By:
Good morning! I am Ryan Stanton, a member of Dr. Shuo Gu's research group within the RNA Biology Lab at NCI-Frederick. Here, we study microRNA modifications and their affects on the molecules' targeting, stability, and turnover. I contribute through building new molecular tools to determine the target repertoires of individual microRNAs. Because this work will require a great deal of RNA-seq down the line, I hope to get experience in using the command line in Unix and developing analysis tools from this course. Thank you, and I look forward to learning with you all!
   View 1 Answer

March 30th, 2021

Can we have a brief introduction of types of data in Bioinformatics?

Views: 4334   Asked By:
I realize Bioinformatics can be applied in different areas with various types of data, such as omics data, RNA-Seq data, next-generation seq data, etc. Can you discuss what's the difference of these data? What are some common steps to analyze them? It would be helpful if you can give us some examples that we may be able to apply in research after the course. Thank you!
   View 1 Answer

March 30th, 2021

Introduction

Views: 4465   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.

   View 1 Answer

March 30th, 2021

Introduction - Corey Young

Views: 4725   Asked By:
I am in DCEG-BB. I have some experience with RNA sequencing data and linux but I would like to get a refresher in some of the software used and the coding involved. My current project focuses on lung cancer screening in special populations and calculating risk of lung cancer in there's populations. 
   View 1 Answer

March 30th, 2021

Will we cover R/Python for bioinformatics in this course?

Views: 5236   Asked By:
Hello! I am Deondre Jordan. I am working for Jay S. Schneekloth in a chemical biology labratory, focused on developing small molecules to bind RNA targets in cancer. I am excited to learn bioinformatics as I have very little experience in this realm of data science.
   View 1 Answer

March 30th, 2021

Introduction

Views: 4913   Asked By:
Hi I'm Meredith and I work in the LCIM in Dr. Howard Young's lab. My research is on the role of regulatory T cells in our mouse model of lupus, and I'm hoping to learn how to generally work with Unix in this course.
   View 1 Answer

March 30th, 2021

how can i get help in this class?

Views: 4574   Asked By:
When are the help sessions?
   View 1 Answer

March 30th, 2021

Analyzing Short/Long read sequencing results and interpreting splicing events.

Views: 4967   Asked By:
I am a post-bac in DCEG. I am using sequencing data to analyze functional consequences of Insilico discovered novel variants in our patient cohort. I'd like help in using software to analyze the sequencing data and splicing events.
   View 1 Answer

February 23rd, 2021

Trouble building CTAT custom genome

Views: 4860   Asked By:
Hi, I am looking into gene fusions in several canine tumors and plan on using STAR FUSION. As I understand first I need to build a CRTA genome. I have been following https://github.com/NCIP/ctat-genome-lib-builder/wiki as a resource but have been unable to get it to run. I keep on getting a error "died with ret 9 No such file or directory at /data/mannheimerjd/sfusion/ctat-genome-lib-builder/lib.Pipeliner line 186" In the code preceding the error message it seems to be trying to find my GTF file. However, the GTF file is in the current working directory and I do not understand why it cannot find it.  any help would be much appreciated. 
   View 1 Answer

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: 5224   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: 4826   Asked By:

July 29th, 2020

What is Cell Ranger?

Categories: Single-Cell RNA-Seq

Views: 4866   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: 4784   Asked By:
What are the differences in how the raw data is handled? What should we expect in how the data may look different at the QC metric stage from whole cell single cell RNA-Seq? Do any adjustments need to be made for analysis pipelines?
   View 1 Answer

July 25th, 2020

Can you say something about trajectory analysis vs. velocity analysis?

Categories: Single-Cell RNA-Seq

Views: 11826   Asked By:
The question from Steve
   View 2 Answers

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: 6026   Asked By:
The question from Lirong
   View 2 Answers

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: 5696   Asked By:
Which large data sets like Tabula Muris are available for cell type identification? What are the tools I can use to identify different cell types in my data? How do these tools work?
   View 1 Answer

July 18th, 2020

What sequencing depth do I need for scRNA-Seq samples?

Categories: Single-Cell RNA-Seq

Views: 6577   Asked By:
What are the considerations for deciding how deeply to sequence a scRNA-Seq sample?
   View 2 Answers

July 18th, 2020

When should we batch correct scRNA-Seq data? When should we avoid it?

Categories: Single-Cell RNA-Seq

Views: 17961   Asked By:
When should we 'batch correct' scRNA-Seq data? When should we avoid it? How do we know when it is appropriate and when it isn't? Is there a difference between 'batch correction' as employed for bulk RNA-Seq and those for scRNA-Seq? Should we distinguish between 'batch correction' and 'dataset alignment'? When is one appropriate over the other? What are the tell-tale signs of an 'overcorrected' batch correction? Do underlying counts matrices ever get modified, or it the modification only for the reduced dimension matrix and resulting clustering and visualizations? Is downstream differential expression testing or things like trajectory modeling performed on the modified or original matrix? 
   View 2 Answers

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: 9030   Asked By:
What is the difference between high throughput single cell methods like droplet-barcoding (like 10x Genomics Chromium) and plate-based methods (ike 'Smart-Seq")? Which is more sensitive? What is the comparative cost of each? 
   View 1 Answer

July 18th, 2020

Difference between 3' and 5' gene expression profiling? Which should I use?

Categories: Single-Cell RNA-Seq

Views: 13277   Asked By:
For those looking to utilize high-throughput gene expression profiling methods that employ a transcript 'end-counting' strategy, one choice that has to be made is whether to employ a 3' chemistry or a 5' chemistry. Knowing when these are typically employed and what limitations each may have are an important early step in planning a single cell RNA-Seq study. What is the difference between 3' and 5' gene expression profiling? Which should be used in which scenario?
   View 2 Answers

July 17th, 2020

questions related to single cell ATAC-seq?

Categories: Single-Cell RNA-Seq

Views: 2441   Asked By:
single cell ATAC-seq and single nucleus ATAC-seq are same or different? single cell ATAC-seq is feasible to apply on cryopreserved tissue sample or single cell suspension? Usually, how many cells are necessary to get enough information for one sample in single cell ATAC assay?
   View 3 Answers

July 17th, 2020

a few experimental design-related questions on single cell RNA-seq?

Categories: Single-Cell RNA-Seq

Views: 2732   Asked By:
  1. 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.
    1. 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.
    2. 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?
    3. 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?
    4. 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?
    5. 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?
  2. 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)
   View 6 Answers

July 16th, 2020

How many cells can I capture in my experiment?

Categories: Single-Cell RNA-Seq

Views: 2115   Asked By:

July 16th, 2020

Which cell types can be used in Single-Cell RNA Seq?

Categories: Single-Cell RNA-Seq

Views: 1648   Asked By:

June 17th, 2020

Local vs. global alignment

Categories: BIOSTAR

Tags: alignment

Views: 5908   Asked By:
How do we decide if we should use local or global alignment?
   View 1 Answer

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: 2205   Asked By:
Should we always use histone markers just to see if our sequencing is working for our samples?
   View 1 Answer

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: 2099   Asked By:
What do you think about ChIP-seq with proteins that are highly mobile in nature? Why is there less data published about using them?
   View 1 Answer

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: 2120   Asked By:
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?
   View 1 Answer

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: 2109   Asked By:

What is a good website to check for transcription factor binding motifs and how they regulate expression?

   View 1 Answer

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: 2039   Asked By:
Do you have recommendations for frameworks or programs for integrating ChIP-seq and RNA-seq or microarray data?
   View 1 Answer

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: 2923   Asked By:
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?
   View 1 Answer

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: 3016   Asked By:
If my replicates are highly reproducible, is it valid to merge my replicates before finding peaks?
   View 1 Answer

June 5th, 2020

Peak calling and analyses: What do you think about ChIPseeker for annotation?

Categories: ChIP-Seq Data Analysis

Views: 2415   Asked By:
What do you think about ChIPseeker for annotation?
   View 1 Answer

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: 2972   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?

   View 1 Answer

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: 2196   Asked By:
If the control is input, which method peak calling do you prefer?
   View 1 Answer

June 5th, 2020

Peak calling and analyses: What peak caller is good for broad peaks?

Categories: ChIP-Seq Data Analysis

Views: 2296   Asked By:
What peak caller is good for broad peaks?
   View 1 Answer

June 5th, 2020

Pipelines and QC:What package do you use to perform a partial duplicate removal?

Categories: ChIP-Seq Data Analysis

Views: 2175   Asked By:
What package do you use to perform a partial duplicate removal?
   View 1 Answer

June 5th, 2020

Pipelines and QC: Does the mouse genome have a blacklist file?

Categories: ChIP-Seq Data Analysis

Views: 2307   Asked By:
Does the mouse genome have a blacklist file?
   View 1 Answer

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: 3743   Asked By:
When and how do you remove blacklisted regions? What program do you use?
   View 1 Answer

June 5th, 2020

Pipelines and QC: What is "effective genome size"?

Categories: ChIP-Seq Data Analysis

Views: 2279   Asked By:
What is "effective genome size"?
   View 1 Answer

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: 962   Asked By:
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?
   View 1 Answer

June 5th, 2020

Pipelines and QC: What are "no hits" on a multiQC report? Are they all adaptors?

Categories: ChIP-Seq Data Analysis

Views: 1054   Asked By:
What are "no hits" on a multiQC report? Are they all adaptors?
   View 1 Answer

June 5th, 2020

Pipelines and QC: What is the average length of a read produced by ChIP-seq?

Categories: ChIP-Seq Data Analysis

Views: 927   Asked By:
What is the average length of a read produced by ChIP-seq?
   View 1 Answer

June 5th, 2020

Pipelines and QC: What is a good mapping percentage?

Categories: ChIP-Seq Data Analysis

Views: 1082   Asked By:
What is a good mapping percentage?
   View 1 Answer

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: 980   Asked By:
Which ChIP-seq pipelines mentioned in your talk can handle paired-end reads?
   View 1 Answer

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: 3429   Asked By:
What is CUT & RUN? How do you compare ChIP-seq and CUT & RUN?
   View 1 Answer

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: 2945   Asked By:
What are the advantages and disadvantages of using ChIP-seq instead of ATAC-seq?
   View 1 Answer

June 5th, 2020

Spike-ins: At what stage of the ChIP experiment do you introduce the spike-ins?

Categories: ChIP-Seq Data Analysis

Views: 986   Asked By:
At what stage of the ChIP experiment do you introduce the spike-ins?
   View 1 Answer

June 5th, 2020

Spike-ins: Can you please give me more detail on how the spike-in works?

Categories: ChIP-Seq Data Analysis

Views: 1227   Asked By:
Can you please give me more detail on how the spike-in works?
   View 1 Answer

June 5th, 2020

Spike-ins: How much spike-in is a good amount to use?

Categories: ChIP-Seq Data Analysis

Views: 1044   Asked By:

How much spike-in is a good amount to use?

   View 1 Answer

June 5th, 2020

Spike-ins: What is a good spike-in sample for ChIP-seq?

Categories: ChIP-Seq Data Analysis

Views: 1146   Asked By:
What is a good spike-in sample for ChIP-seq?
   View 1 Answer

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: 824   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?

   View 1 Answer

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: 1041   Asked By:
Can you use ChIP-seq data to analyze copy number variants? Can you do structural variant calling?
   View 1 Answer

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: 1218   Asked By:

How do I choose between sonication and enzymatic-based chromatin fragmentation for ChIP-seq? How might this affect sequencing depth?

   View 1 Answer

June 5th, 2020

Library ChiP preparation: Is the sequencing depth based on the organism you're working with?

Categories: ChIP-Seq Data Analysis

Views: 974   Asked By:
Is the sequencing depth based on the organism you're working with?
   View 1 Answer

June 5th, 2020

Library ChIP preparation: What happens if there are too many PCR cycles?

Categories: ChIP-Seq Data Analysis

Views: 1096   Asked By:
What happens if there are too many PCR cycles?
   View 1 Answer

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: 959   Asked By:
What should be the starting amount of DNA for fresh and fixed sample?
   View 1 Answer

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: 995   Asked By:
Can ChIP-seq be done on formalin fixed tissue and if yes how much starting material is usually required?
   View 1 Answer

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: 1142   Asked By:
Is it okay to use frozen samples or is it better to use fresh cells?
   View 1 Answer

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: 940   Asked By:
What if my antibody has low binding affinity and there isn't a better option available?
   View 1 Answer

June 5th, 2020

Library/ChIP preparation: What are nanobodies? Can they be used for ChIP-Seq?

Categories: ChIP-Seq Data Analysis

Views: 2277   Asked By:

What are nanobodies? Can they be used for ChIP-Seq?

   View 1 Answer

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: 899   Asked By:

Is there a bias with ChIP-Seq data because promoters tend to be GC-rich and tend to be open chromatin regions?

   View 1 Answer

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: 1344   Asked By:
Is it ever useful to do a non-specific antibody first, then a specific antibody?
   View 1 Answer

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: 1142   Asked By:
Why does my IgG control sample have higher binding than the antibody binding sample for qPCR? What do I do about it?
   View 1 Answer

June 5th, 2020

Control Types: Is there a reason not to use both IgG and Input controls?

Categories: ChIP-Seq Data Analysis

Views: 983   Asked By:
Is there a reason not to use both IgG and Input controls?
   View 1 Answer

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: 2442   Asked By:
Under what conditions is it better to use the Input versus IgG control for ChIP-Seq?
   View 1 Answer

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: 868   Asked By:
What is copy number bias? How are we supposed to address it for ChIP-Seq?
   View 1 Answer

June 5th, 2020

Control Types: What is the difference between input and naked DNA?

Categories: ChIP-Seq Data Analysis

Tags: chipseq

Views: 1330   Asked By:

What is the difference between in put and naked DNA?

   View 1 Answer

June 4th, 2020

Issues with installing jellyfish on a MAC computer

Categories: BIOSTAR

Tags: jellyfish install mac

Views: 2115   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

   View 2 Answers

May 28th, 2020

Control Types: Can we use any DNA-seq as an input sample?

Categories: ChIP-Seq Data Analysis

Tags: chip-seq

Views: 1254   Asked By:

Can we use any DNA-seq as an input sample?

   View 1 Answer

May 21st, 2020

Lecture recording and notes

Categories: BIOSTAR

Views: 2068   Asked By:

Are our lectures/classes recorded, and if so where can we access them?

   View 1 Answer

May 13th, 2020

Error using parallel tool for fast-dump

Categories: BIOSTAR

Views: 2193   Asked By:
Hi, I tried to run the following command
cat runids.txt | parallel fastq-dump -X 10000 --split-files
and got an error message about int: buffer insufficient / cannot get cloud location / timeout exhausted (see attached screen grab). Is it something to do with my PC memory or bandwidth perhaps? Thanks, Jo  
   View 1 Answer

May 13th, 2020

CSVKit issue in biowulf

Categories: BIOSTAR

Views: 2114   Asked By:
Hi I was using csvkit in biowulf's sinteractive session. Everytime when I use csvcut, a warning message pops out 'WARNING: Bind mount '/data => /data' overlaps container CWD /data/yangz13/biostar_class/sra_runs, may not be available'. Does this mean that I did something wrong? Thanks
   View 1 Answer

May 10th, 2020

How to quickly activate bioinfo in biowulf?

Categories: BIOSTAR

Views: 2016   Asked By:
I have installed the bioinfo package in my own data directory. Right now, every time when I open a new terminal window, I have to enter the two commands below
[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
   View 1 Answer

April 30th, 2020

what does -f stand for in the bash profile setup?

Categories: BIOSTAR

Tags: Unix

Views: 3847   Asked By:
Hi. Could you please help to explain what is the meaning of [-f ~/.bashrc] in the bashprofile setup below? Thanks
#
if [ -f ~/.bashrc ]; then
   source ~/.bashrc
fi

   View 1 Answer

April 27th, 2020

What are the Rules and Purpose of this Forum

Views: 1909   Asked By:
What are the Rules and Purpose of this Forum
   View 1 Answer

April 24th, 2020

Error in library(DESeq)

Categories: BIOSTAR

Views: 3210   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-gplots
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April 23rd, 2020

how to use commend lines to do data analysis?

Categories: BIOSTAR

Views: 1823   Asked By:
Hi there, I have two questions:
  1. 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? 
  2. 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. 
  thanks a lot!
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April 23rd, 2020

How to do the exercise from the book with Chr22 and hg38 but with hg37

Categories: BIOSTAR

Views: 2118   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

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April 22nd, 2020

Can you recover a removed file after issuing the rm command?

Categories: BIOSTAR

Tags: Unix

Views: 2099   Asked By:

Can you recover a removed file after issuing the rm command?

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April 22nd, 2020

How to enable colors for the ls command

Categories: BIOSTAR

Views: 1151   Asked By:
How do we get the "ls" command to print out directories/files in different colors?
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April 22nd, 2020

Customizing your terminal prompt?

Categories: BIOSTAR

Tags: Unix

Views: 1943   Asked By:

April 21st, 2020

efetch, bgzip, infoseq, seqkit, bioawk – commands not found. Do I need to install something?

Categories: BIOSTAR

Views: 2951   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?

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April 20th, 2020

Asking before deleting

Categories: BIOSTAR

Views: 1085   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

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April 16th, 2020

Makefile target command problems

Categories: BIOSTAR

Views: 1335   Asked By:
Hi All, I've tried the Using Makefiles: What is a makefile section but was unable to execute the "foo" and "bar" targets properly. I have attached a screen grab of what I tried to do. I kept getting a command not found error.. Does anyone know where I went wrong? I've tried adding 'makefile' in front and I get the same error message.   Thanks in advance! Jo
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April 14th, 2020

trouble installing makefiles

Categories: BIOSTAR

Views: 1839   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)

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April 12th, 2020

Ubuntu on Windows installation issues

Categories: BIOSTAR

Tags: Ubuntu on Windows

Views: 1915   Asked By:
Hi, I was trying to install Ubuntu Linux on Windows but it gives me an error that the program requires me to enable the Windows Subsystem for Linux. I am not able to do this. I tried to follow instructions from https://docs.microsoft.com/en-us/windows/wsl/install-win10?redirectedfrom=MSDN, but it gives me an error. I do not think my admin allows me to do this. I submitted a ticket to NIH Help desk to see if they can help me with this, but I was wondering if anyone else found this issue.
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April 9th, 2020

How to install Ubuntu if you are located at NCI Frederick

Categories: BIOSTAR

Tags: Ubuntu

Views: 1113   Asked By:
Hi, I can't get permission to install Ubuntu on my PC. What should I do?
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April 9th, 2020

Ubuntu Linux on Windows link

Categories: BIOSTAR

Views: 1385   Asked By:
Hi, can you share the Ubuntu link that does not go to the windows store? Thanks.
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April 9th, 2020

The miniconda download does not work!

Categories: BIOSTAR

Tags: miniconda

Views: 1588   Asked By:

It does not download, I just get an error message. 
 

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April 9th, 2020

More trouble with Xcode

Categories: BIOSTAR

Views: 1400   Asked By:
I have downloaded an older version of Xcode, extracted the software and then moved it to my Applications folder. However, when I try to continue with the set up instructions (typing “xcode-select —install”) I receive the error message “Can’t install the software because it is not currently available from the software update server.” It looks like my Xcode is definitely installed and located in “/Applications /Xcode.app/Contents/Developter” instead of in “/Library/Developer/CommandLineTools”  If I try to proceed with installing Homebrew, I receive the same error message about Xcode. What should I do?
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April 7th, 2020

Administrator issues with PC government computer

Categories: BIOSTAR

Views: 2202   Asked By:

How will I be able to install the programs on the PC government computer?

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April 6th, 2020

MacOS users: Where to find older versions of XCode?

Categories: BIOSTAR

Views: 23845   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?

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April 2nd, 2020

Which shell to use for Mac OS Catalina (10.15.*)

Categories: BIOSTAR

Views: 1564   Asked By:
In the Biostar handbook the instructions say I should change the default shell from zsh to bash,  do I really need to do this and what are the consequences, or side effects?
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April 2nd, 2020

What are the Rules and Purpose of this Forum

Categories: BIOSTAR

Tags: Rules

Views: 5302   Asked By:
What are the Rules and Purpose of this Forum
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April 2nd, 2020

What is the difference between RPKM, FPKM and TPM

Categories: FAQ

Tags: RNA-Seq

Views: 79923   Asked By:
When analyzing RNA-Seq data what is the difference between RPKM, FPKM and TPM… and why should I care.
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