Questions tagged [bash]

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2answers
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Changing this code in a way to work for my files

I have a bash script which extracts some information from a .vcf file but one .vcf file at each time. How I can change this script in a way to work on a bunch of .vcf files and the output is a .txt ...
2
votes
1answer
48 views

How to edit the headers of multiple fasta files from multiple folders?

My directories are organized as follows: one main directory, in which I have multiple directories that end with a number ranging from 314 to 727, followed by .3 . For example, 'mgm4761314.3'. Within ...
0
votes
2answers
94 views

Looping over several files in bash

I have a bash script: I am wondering how I can change this script to loop over a bunch of .vcf files and give output .txt with the name of corresponding .vcf I tried changes done in similar script ...
3
votes
3answers
82 views

How to get the product of a CDS

I need the name of the protein in /product="protein_name" using bash commands. Beware, there is a lot of whitespace between lines. ...
1
vote
2answers
363 views

How to merge .fastq.qz files into a single .fastq.gz with their same id without losing any content in parallel

I have a large number of .fastq.gz files of different lane and reads. I have to merge them each reads group files into single .fastq.gz files. **eg: 1st type NA24694_GCCAAT_L001_R1_001.fastq.gz ...