Questions tagged [shell]

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panX installation error

I tried to install panX tool (pan-genome analysis tool) in my computer (Ubuntu 16.04 LTS, 64 bit version). I have followed all the steps mentioned in the manual. finally I ran the test data by ...
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19 views

Command-line blastn not responding; trace says “Resource not available”

I hadn't used the NCBI command-line tools for a while, and just got back into it. But no matter where or how I run blastn now, I get an almost complete lack of response: just the initial "BLASTN ...
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1answer
88 views

awk shell script

I have a folder named quant. Inside this folder I have 27 folders named SRR8068516_quant to SRR8068543_quant. I want to edit a file inside these folders titled quant.sf and produce an output. I ...
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1answer
99 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 ...
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1answer
55 views

processing multiple fastq files with cutadapt

I have DNA sample from 5 pools, having 25 fastq files each. I am running cutadapt to remove the primers using this command ...
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1answer
32 views

gnu parallel for macs peak calling

These are the list of files ...
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1answer
57 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 ...
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0answers
26 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, ...
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1answer
41 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: ...
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2answers
77 views

How I can run this code on my files?

I am annotating some .txt files by Annovar software by this code nnovar]$ module load annovar/2016Feb01 [cyan01 annovar]$ table_annovar.pl But I really got ...
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1answer
47 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 ...
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2answers
251 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 ...
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4answers
153 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 ...
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1answer
56 views

Pattern mining from a genomic sequence

I need to find the following pattern from a genomic sequence ...
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1answer
351 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: ...
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3answers
490 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 ...
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1answer
58 views

Regular expression struggle

These are my files ...
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2answers
970 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 ...
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1answer
319 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
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1answer
122 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
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1answer
158 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, ...
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0answers
43 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 ...
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1answer
1k 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 ...
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0answers
71 views

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

I am learning about vcf file formatting and have a multi-sample (>300) vcf file and aim to group (take) samples with shared mutations. Can someone suggest a tool/command/script solve this problem?
5
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1answer
88 views

Bash script error at paste command

I wrote script for pasting rsids on CADD output. Here is script. ...
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3answers
147 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
289 views

How do I filter a GFF file by gene type?

I have a file with following information: ...
5
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5answers
8k 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
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1answer
359 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. (...
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4answers
438 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 ...
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5answers
533 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 ...