Questions tagged [shell]

The tag has no usage guidance.

Filter by
Sorted by
Tagged with
1
vote
1answer
55 views

move files of a different group to separate directory

EDITED I have list of my samples in first column and corresponding file name for my .vcf files in second column of a file name clin_name.txt like below. For ...
0
votes
0answers
36 views

what is the best option for genomic analysis? [closed]

It is best to work with PowerShell, shell script, Pycharm or R for analysis and alignment with Python and R programming language, focusing on genomic analysis, CDS (statistical analysis, database) ...
0
votes
0answers
19 views

running MAFFT on windows git bash

I'm pretty new to bioinformatics, I got some shell scripts from a senior who used to do things that I need to do, but these scripts were written on a Mac and I'm trying to set it up for Windows, ...
1
vote
1answer
21 views

Fastq-dump script download X spots or all

Im trying to write a script where an optional input of -X flag can be used, or if that info is not available download all reads. my script as follow: ...
0
votes
2answers
54 views

How I can run this code on my files?

I am annotating some .txt files by Annovar software by this code ...
0
votes
1answer
23 views

Peak-calling using homer

I have a total of 78 ATAC seq samples from which Im trying to do a peak call .I tried this batchParallel.pl findPeaks peaks function but i couldn't find the output ...
0
votes
2answers
174 views

How to loop multiple function in shell script?

I need to extract sequences one after another consecutively from a large fasta files (multiple fasta files) and each extracted files to be saved in new fasta file (I mean the first sequence extracted ...
1
vote
4answers
100 views

How I can change the name of multiple files at once in R or terminal?

I have 200 .vcf files in a folder with long names like LP6005409-DNA_E03_vs_LP6005408-DNA_E03.snp.pass.vcf How can I change the name of each file to, for ...
2
votes
1answer
48 views

Pattern mining from a genomic sequence

I need to find the following pattern from a genomic sequence ...
1
vote
1answer
80 views

for loop cutadapt for files on a single directory

I have a bigfolder where i have a lot of fastq.gz files and I want to remove the adapters from all of them. I am trying then the following loop: ...
2
votes
3answers
254 views

How to reverse complement the DNA sequences for given inverse/reverse coordinates?

I have the series of coordinates in id.txt file, whose coordinates sequences are in genome.fasta file. The coordinates of id.txt ...
-1
votes
1answer
50 views

Regular expression struggle

These are my files ...
1
vote
2answers
240 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
148 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 ...
2
votes
1answer
62 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
69 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
vote
0answers
40 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
votes
1answer
651 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
votes
0answers
48 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
80 views

Bash script error at paste command

I wrote script for pasting rsids on CADD output. Here is script. ...
2
votes
3answers
143 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
votes
1answer
162 views

How do I filter a GFF file by gene type?

I have a file with following information: ...
3
votes
5answers
5k 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. <...
8
votes
1answer
246 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
311 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
votes
5answers
479 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 ...