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12 votes
5 answers
23k views

How to download FASTA sequences from NCBI using the terminal?

I have following accession numbers of the 10 chromosomes of Theobroma cacao genome. ...
MudithMMBc's user avatar
9 votes
5 answers
1k 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 ...
EMiller's user avatar
  • 483
8 votes
7 answers
2k views

What are the available cloud computing services for bioinformatics? [closed]

I'm looking for cloud computing services that can be used for doing bioinformatics. An example I found is InsideDNA and there is Amazon of course. A little description of these would be appreciated.
Peter's user avatar
  • 2,634
6 votes
2 answers
430 views

Parallel processing of scripts that use obitools

I have an obitools script (de Barba et al. 2016) that I would like to run faster. How would you run it in parallel to cut down on time? ...
Roman Luštrik's user avatar
5 votes
3 answers
2k views

Removing duplicate FASTA sequences based on headers with Bash

I used the following command to remove duplicate FASTA sequences based on the header sequence: ...
aman's user avatar
  • 51
5 votes
3 answers
1k views

finding unique headers in a fasta file using linux command line

I tried to use the following command uniq -u reference.fasta >> reference_uniq.fasta I'd like a count of the unique headers.
crispr's user avatar
  • 51
4 votes
3 answers
326 views

How to retrieve sequences from a txt file by protein names from other txt file?

My problem is that I want to retrieve the sequences line + secondary structure line that match the protein names from the header.txt file: The text file(...
Amal's user avatar
  • 81
4 votes
2 answers
3k views

Installing DESeq2 in Ubuntu

I am trying to install DESeq2 in my Ubuntu with R version 3.5.1. According to the package repository in Bioconductor the version should be 3.5. ...
aerijman's user avatar
  • 645
4 votes
4 answers
1k views

How to get a file with the number of reads for several fastq.gz files?

I have generated several FASTQ files and I would like to know the amount of reads for each of them. I am planning to run FastQC on the files which I know would give me the number of reads per sample ...
pythonbeginner's user avatar
3 votes
4 answers
2k views

How to run same command on multiple files?

Hi im doing Variant calling on fastq files for which i have 4000 fq files and the variant calling are done in different 9 steps. Each step generate different files that are output to next steps. So ...
Safina A.R's user avatar
3 votes
2 answers
845 views

Downloading multiple SRA files from several SRA accession IDs does not work

I am trying to download multiple SRA files located in several SRA accessions. Some of my accession numbers are as follows: ...
Safina A.R's user avatar
3 votes
3 answers
84 views

How to copy only certain counts for genes in tsv file to new file in linux

Hi there I have generated a counts table of samples I need to compare by differential expression analysis. The layout of the counts table is as follows: Gene_id Sample_A_r1 Sample_A_r2 Sample_B_r1 ...
Justin1609's user avatar
3 votes
3 answers
148 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. ...
Aron van Beelen's user avatar
3 votes
1 answer
96 views

Extract specific nucleotide base position for query and subject from text file

I have an input file looks like this: ...
user14714429's user avatar
3 votes
1 answer
512 views

How to extract exome on-target reads in batch?

I was given a list of target regions in BED and many exome alignments in BAM. I was asked to extract on-target alignments from these BAMs to save disk space. I know I can use bedtools to extract sub-...
medbe's user avatar
  • 847
3 votes
2 answers
672 views

How to remove sequences from a fasta file using a sequence ID list which contains a space within the id?

I have a fasta file that contains sequence reads and sequence id file that needed to be removed from the fasta file. I have done this earlier, but since id contains a space my piece of code is not ...
MudithMMBc's user avatar
3 votes
1 answer
240 views

How to submit a canu job on LSF high-performance computing cluster farm?

I am currently running canu on an LSF Linux server using the following script called assemble.sh: ...
Biomagician's user avatar
  • 2,459
3 votes
1 answer
362 views

"perl: warning: Setting locale failed." in RepeatMasker

I'm trying to run Repeatmasker in Linux on the command line with: ...
RNAdey's user avatar
  • 31
2 votes
4 answers
481 views

How to make work programs from the $PATH?

I am trying to analyze my RNAseq reads for defective genomes and I use this program (http://www.di-tector.cyame.eu/) that is suggested by Beauclair et al (https://pubmed.ncbi.nlm.nih.gov/30012569/) ...
Dmitrii Trubetskoy's user avatar
2 votes
2 answers
169 views

How can I run a command for multiple files?

I have a bunch of .vcf files in a folder and I want to run command below on all of them but doing that one by one manually is really painful. I am seeking for a way ...
user avatar
2 votes
1 answer
62 views

How to loop over certain files within a directory that belongs to certain samples

This question was also asked on Biostars I have two samples where the sequencing was done on 3-lanes paired end reads. The two samples are A44943_1 and A44944_1. I would like to generate a for in loop ...
Mohamed Samir's user avatar
2 votes
3 answers
191 views

How do I find unique file names without their extensions in shell script?

I need to generate a list of unique file names without their extensions or using the shell script command "find" Say I have a list such as: ...
Lou_A's user avatar
  • 361
2 votes
1 answer
1k views

How do I filter a GFF file by gene type?

I have a file with following information: ...
stack_learner's user avatar
2 votes
2 answers
156 views

Mapping to assemblies in subdirectories

I am performing a bash loop one liner:. for k in */Assembly/*/*.fastq; do minimap2 -ax map-ont assembly.fasta $k > mapping.sam; echo $k; done The file hierarchy ...
matt's user avatar
  • 21
2 votes
1 answer
2k views

Error in installing Vep

I am trying to installing Vep on Linux but an error is permanent ...
Zizogolu's user avatar
  • 2,160
1 vote
4 answers
2k 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 ...
Zizogolu's user avatar
  • 2,160
1 vote
4 answers
5k views

Edit FASTA header using sed

I need to rename the following headers from a FASTA file. Something like: ...
taeju's user avatar
  • 21
1 vote
2 answers
3k views

Running MaxQuant on Linux

I'm trying to run MaxQuant on a linux laptop, hower I'm constantly running into problems with MaxQuant crashing at different stages I tried to use mono 6.8 mono 5.4.1 on centos ubuntu each with ...
Manuel's user avatar
  • 113
1 vote
2 answers
63 views

Moving file based on their names

I have a list of vcf files; I also have a list of names in a txt file like LP6005409-DNA_F01 LP2000325-DNA_A01 LP6005409-DNA_E02 LP6005500-DNA_C03 What I have in ...
Zizogolu's user avatar
  • 2,160
1 vote
2 answers
41 views

Print first colum is the condition is true using awk

I have a binary file which looks like this, ...
ambika's user avatar
  • 23
1 vote
2 answers
234 views

Pulling a numbered chromosome range file given a gene location from a lookup table ideally from command line or R

have a folder with roughly 1000 vcf files which have divided the human genome into chunks, the folder looks like this: ...
tacrolimus's user avatar
1 vote
1 answer
108 views

How do I remove allele annotations from SNP Ids in .bim file?

Hello every one i need help in editting my .bim file. So my .bim file looked like following. I want to convert the ids with chromosomal position from chr1_867635_C_T...
Aryh's user avatar
  • 127
1 vote
2 answers
84 views

How to parse hmmsearch output?

I did hmmsearch with --notextw and --domtblout and I see several results for ids, I want to ...
bobr's user avatar
  • 11
1 vote
1 answer
74 views

Copying files from multiple directories to a single

I have multiple .GFF files, each in a single directory per annotated whole genome, that I wish to copy into a single directory so that I can perform a core genome alignment. However the following code ...
MicroBiostat's user avatar
1 vote
1 answer
202 views

how to sort and join two files based on First Column Id

I have got two files large files like this in Tab-delimited format, trying to merge in R, do we need to sort the file before merging? ...
bioinfonext's user avatar
1 vote
1 answer
662 views

How do I build the "Standard Kraken 2 Database"?

I am at this point in the GitHub tutorial: https://github.com/DerrickWood/kraken2/blob/master/docs/MANUAL.markdown#standard-kraken-2-database It says to create the standard Kraken database, I use the ...
InterestingPenguin80's user avatar
1 vote
1 answer
111 views

Convert Arlequin ("DNA" markers) to Genepop (PGDspider or otherwise)

I have Arlequin output files (*.arp) from fastSimcoal2 that I'm trying to convert to genepop files (to read into adegenet). The Arlequin files are using the "DNA" marker (50 bp long), and ...
akoontz11's user avatar
  • 123
1 vote
1 answer
518 views

Compare mapped reads from BWA -MEM and STAR from .bam files

I want to find and compare the results from STAR and BWA- MEM mapped. I have 150bp paired end reads in sorted.bam files in each case and i want to find in each case uniquely mapped reads, number of ...
user3683485's user avatar
1 vote
1 answer
61 views

What are Dummy fastqs?

I had to do a file transfer for in our system to run from fastqs and I came across the term "dummy fastq", not sure what exactly it means and what is the purpose of it in the workflow. Can ...
Navya's user avatar
  • 19
1 vote
3 answers
1k views

Concatenate multiple fasta files into one file for MLST

I have seven fasta files, one per gene, with more than 400 fasta entries per file, like this: Input: Gene1.fasta ...
Saruul B's user avatar
1 vote
1 answer
38 views

Increasing memory usage in AWS instance

I have 16 CPUs on my AWS EC2 instance and I am trying to use kSNP4 to generate an SNP matrix. I was able to successfully run this with over 150 samples - while it took a while to run it did complete - ...
rimo's user avatar
  • 1,003
1 vote
1 answer
144 views

How to use Gblocks for trimming single-copy gene sequences?

I have run OrthoFinder on a set of 11 genomes and got the results in a folder. From the output folder, I saved all the single-copy gene sequences in a single FASTA file and now wish to remove all gaps ...
K_081's user avatar
  • 149
1 vote
1 answer
70 views

bsub with -M and -hl a good idea?

I have been submitting my snakemake pipeline to a node-shared high performance computer (HPC) via bsub the following way: ...
Dandelion's user avatar
  • 313
1 vote
3 answers
225 views

Finding smaller sequences from within larger sequences

I am currently working with fastq files which have hundreds of thousands of lines of text. However, not all of them are sequences I am interested in. My sequences are in one line and have a fixed ...
Jean Luc's user avatar
1 vote
1 answer
45 views

Add segregating sites to branches of a tree

I'm trying to figure out how I would plot a tree with number of segregating sites on display on the branches I'm using acctran from phangorn to plot a parsimony tree (using phydat object from fasta ...
AWE's user avatar
  • 121
1 vote
2 answers
659 views

processing fastq files using cellranger on linux

I am trying to perform a cellranger count on fastq files generated from a 10x genomics single cell RNA Seq run. Just to provide some background, I ssh’d into the AWS using our AWS IP with MobaXTerm ...
sv1234's user avatar
  • 29
1 vote
1 answer
554 views

Why is my STAR reference genome indexing aborting on my GNU/Linux server but not on my Mac OS X laptop?

I am running the following command to index my genome: ...
Biomagician's user avatar
  • 2,459
1 vote
0 answers
24 views

OsError in virtual box snakemake pipeline for array-analysis

The rule is written for calling genotypes using array analysis cli for illumina gsa chips. ...
lesserFlamingo's user avatar
1 vote
0 answers
195 views

Removing adapters + primers from fastq files

I am currently in the process of removing adapters and primers from some 16S data acquired, and have a conceptual question regarding this pre-processing step: So there are a series of different primer ...
h3ab74's user avatar
  • 846
1 vote
1 answer
1k views

Searching for adapter sequences in FASTQ files - metgenomics

I have recently received some metagenomic data from 16S rrna sequencing. The sequencing company claim to have removed primers, however not adapter sequences. Please note that the files have been ...
h3ab74's user avatar
  • 846