18
votes
Accepted
Using shells other than bash
Bioinformatics tools written in shell and other shell scripts generally specify the shell they want to use (via #!/bin/sh or e.g. ...
- 946
11
votes
Using shells other than bash
TL;DR
SH adheres to an official industry standard, but it is not suitable for scientific computing. Bash is considered an informal standard (e.g., by Google). Bash 3 is preferable in most of ...
- 1,899
10
votes
Accepted
How to run same command on multiple files?
Another solution for repeating one command with different parameters is to use parallel.
Create a tab-delimited file samples.txt...
- 1,342
10
votes
Accepted
How to download FASTA sequences from NCBI using the terminal?
Alternatively, you can use the NCBI Entrez Direct UNIX E-utilities
Basically, you have to download the install file here: https://www.ncbi.nlm.nih.gov/books/NBK179288/bin/install-edirect.sh
In the ...
- 1,021
10
votes
Removing duplicate FASTA sequences based on headers with Bash
If you want to avoid using extra libraries for any reason, you can just use a simple Python script (version 3.6 and above) to do this:
...
- 496
9
votes
What are the available cloud computing services for bioinformatics?
I have trialed the free version of InsideDNA, and these were my notes:
Cost: \$225/month for a team of 5 with 50TB storage or \$45/month with 10TB storage for individuals (assuming 6 month package: ...
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9
votes
How I can change the name of multiple files at once in R or terminal?
Use perl-rename. This is usually called rename on Debian-based systems like Ubuntu or Mint, and ...
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9
votes
Removing duplicate FASTA sequences based on headers with Bash
You can use seqkit for this purpose.
seqkit rmdup -n seqs.fa -o seqs_without_duplicate.fa
- 629
8
votes
8
votes
Edit FASTA header using sed
awk 'BEGIN{FS="::"}{if($1~">"){printf(">%s_%s\n",$2,substr($1,2))}else{print $0}}' input_file.fa > output.fa
An explanation of the non-obvious bits:
<...
- 19.5k
7
votes
Accepted
Script to run everything in a loop for extracting tar.gz files into fastq and to bam with alignment?
This should work for you:
...
- 1,816
7
votes
Using shells other than bash
The Open Group Base Specifications Issue 7
IEEE Std 1003.1™-2008, 2016 Edition, or "The POSIX Standard" for short, is the standard that defines the interfaces and utilities provided by a Unix system. ...
- 171
6
votes
Accepted
Downloading multiple SRA files from several SRA accession IDs does not work
First of all, the brace expansion you tried to use isn't valid. While bash can expand {1..3} to 1 2 3, it has no way of knowing ...
- 9,442
5
votes
How to run same command on multiple files?
if you have a repeating workflow, I strongly recommend to have a look at workflow management systems like snakemake. I've also wrote a little tutorial on biostars about this topic, which might be ...
- 1,342
5
votes
finding unique headers in a fasta file using linux command line
If you just want the number of unique headers, you can do this:
grep '>' reference.fasta | sort | uniq | wc -l
If you want a list of the unique headers, you ...
- 3,141
5
votes
Using shells other than bash
The generic command sh is quite literally an industry standard, a POSIX standard, to be precise (IEEE 1003.2 and 1003.2a, available for purchase for hundreds of ...
- 13.5k
5
votes
Using shells other than bash
I would not say bash as a "standard", but it is indeed likely to be the most widely used unix shell and available by default on most modern unix/linux distros. There are a few other more convenient ...
- 6,435
5
votes
What are the available cloud computing services for bioinformatics?
I'm not sure what kinds of bioinformatics tasks you would like to perform, therefore it is difficult to give a good recommendation.
If you're specifically working on statistical genetics, I can ...
- 241
5
votes
Accepted
How I can change the name of multiple files at once in R or terminal?
just to complete your question, you can do it in R in one line.
After setting the directory as your working directory, just type the following:
...
- 1,021
5
votes
Accepted
5
votes
Accepted
Changing this code in a way to work for my files
Using shell loops for text practice is considered bad practice. It is exceedingly slow, the syntax is complicated so it's very easy to get it wrong and it's just painful. The shell isn't designed as a ...
- 9,442
5
votes
How to get a file with the number of reads for several fastq.gz files?
One way would be to use seqkit stats, which can be installed using conda:
...
- 3,024
5
votes
How to loop over certain files within a directory that belongs to certain samples
You can certainly use a for loop for this if desired, but an easier method is to use the cat command - something like this:
...
- 782
4
votes
What are the available cloud computing services for bioinformatics?
Depending on your applications and uses, you might be interested in checking out CyVerse. It is an NSF funded initiative that provides you with data storage, high performance computing resources, and ...
- 131
4
votes
Accepted
What are the available cloud computing services for bioinformatics?
It really depends on what you are trying to do, but here are a few services that I know of.
GATK on Google Genomics Cloud: Google and the Broad offer a cloud instance tailored to GATK pipelines.
...
- 429
4
votes
Installing DESeq2 in Ubuntu
First I installed this libraries:
sudo apt-get install libcurl4-openssl-dev libxml2-dev
I then installed RCurl:
...
- 635
4
votes
4
votes
Accepted
How to convert mzXML to mzML format (mass spectrometry files)?
ProteoWizard offers this functionality:
msconvert your_mzXML_file --mzML
FileConverter of ...
- 3,892
Only top scored, non community-wiki answers of a minimum length are eligible