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Questions tagged [shell]

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2answers
118 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
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1answer
46 views

removing mitochondrial read and unassembled “random” from multiple bam files

This is the one i used for a single bam file to filter its mitochondrial as well as unassembled read ...
1
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1answer
17 views

Executing PyMOL from a Shell script

I'm trying to execute pymol from a shell script (and it is not working). I'm not executing the script on PyMOL but even if I do this, it doesn't work neither. However, if instead of a script the ...
1
vote
1answer
35 views

Batch alignment of inconsistently named Fastq files

I have numerous gzip-compressed paired-end Fastq files with ChIP-seq data that I would like to align with bowtie2. I confirmed that bowtie2 takes .gz files, ...
1
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0answers
39 views

“Bad substitution” error while trimming adapters [closed]

I have this script to trim adaptors from my fastq sequencing files for PAIR in $(fastq | sed 's/_R.//g' | uniq) I am gitting this error: bad substitution Could ...
4
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1answer
194 views

Splitting fasta file into smaller files based on header pattern

I have to split this fasta files into smaller files and write them into individual files my files ...
3
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0answers
44 views

group samples based on shared mutations in a single multi samples vcf file

I am learning about vcf file formatting and sorry for asking a dumb question. I have a multi-sample (>300) vcf file and I want to group (take) samples with shared mutations. Can someone suggest a ...
5
votes
1answer
67 views

Bash script error at paste command

I wrote script for pasting rsids on CADD output. Here is script. ...
2
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3answers
142 views

Replace lowercase characters with -

I have an output from vcfutils.pl vcf2fq with specified minimal depth, and it means that nucleotides with not enough depth are lowercase. I would like to change them to gaps. I could do it in higher ...
2
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1answer
88 views

How do I filter a GFF file by gene type?

I have a file with following information: ...
3
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5answers
3k views

Remove/delete sequences by ID from multifasta

I have a fasta file like this: >Id1 ATCCTT >Id2 ATTTTCCC >Id3 TTTCCCCAAAA >Id4 CCCTTTAAA I want to delete sequences that have the following IDs. <...
9
votes
1answer
176 views

Using a Bash Script to search TaxIDs against NCBI's Taxonomy yields “400 Bad Request” error?

I've been searching TaxIDs against NCBI's Taxonomy DB to get taxonomic lineages for species. I have successfully done this for 1,000's of TaxIDs that were returned to me by Blast+ blasts in a CSV. (...
12
votes
4answers
289 views

How do I efficiently subset a very large line-based file?

This has come up repeatedly recently: I have a very large text file (in the order of several GiB) and I need to perform line-based subsetting for around 10,000 lines. There exist solutions for ...
9
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5answers
451 views

Using shells other than bash

As someone who's beginning to delve into bioinformatics, I'm noticing that like biology there are industry standards here, similar to Illumina in genomics and bowtie for alignment, many people use ...