Questions tagged [bash]
Use this tag to refer to the questions related to the Linux and Unix shell abbreviated as bash (Bourne Again SHell). It has notable programmatic strengths over C shell (csh) and touch C shell (tcsh)
8
questions
4
votes
1answer
345 views
Error given while trying to index a BAM file with Samtools Index - NO COOR?
I am currently working on my own Metagenomic pipeline, utilizing Bowtie 2 to map. Bowtie 2 outputs a SAM file, which I convert to a .BAM and sort it using Samtools. When I try to utilize Samtools to ...
2
votes
1answer
305 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
124 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 ...
0
votes
2answers
117 views
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 ...
3
votes
3answers
98 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.
...
2
votes
2answers
5k 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
...
1
vote
1answer
613 views
remove sequences from fasta file matching a string in the header
I have a file with 16S sequences. some headers contain species information. For my purposes I would like to exclude a number of species from the file, therefore I would like to do a pattern matching ...
0
votes
2answers
61 views
Print specific columns in a matrix on the basis of sample id's in the header
I have a matrix file (expression.txt) in which the first column is a gene_id and from the second column the sample id's start. This matrix has 20,000 columns with sample id's corresponding to ...
