Questions tagged [linux]
The linux tag has no usage guidance.
71
questions
10
votes
5
answers
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How to download FASTA sequences from NCBI using the terminal?
I have following accession numbers of the 10 chromosomes of Theobroma cacao genome.
...
- 331
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 ...
- 483
8
votes
7
answers
2k
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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.
- 2,604
6
votes
2
answers
408
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?
...
- 241
5
votes
3
answers
2k
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Removing duplicate FASTA sequences based on headers with Bash
I used the following command to remove duplicate FASTA sequences based on the header sequence:
...
- 51
5
votes
3
answers
1k
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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.
- 51
4
votes
3
answers
292
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(...
- 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.
...
- 585
4
votes
4
answers
311
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 ...
- 115
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 ...
- 119
3
votes
2
answers
750
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:
...
- 119
3
votes
3
answers
79
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
...
- 41
3
votes
3
answers
139
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.
...
3
votes
1
answer
68
views
Extract specific nucleotide base position for query and subject from text file
I have an input file looks like this:
...
- 31
3
votes
1
answer
483
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-...
- 777
3
votes
1
answer
228
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:
...
- 2,449
3
votes
1
answer
319
views
"perl: warning: Setting locale failed." in RepeatMasker
I'm trying to run Repeatmasker in Linux on the command line with:
...
- 31
2
votes
4
answers
384
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/) ...
2
votes
2
answers
160
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 ...
user6517
2
votes
3
answers
90
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:
...
- 361
2
votes
1
answer
911
views
2
votes
2
answers
111
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 ...
- 21
2
votes
2
answers
372
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 ...
- 331
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 ...
- 1,797
1
vote
4
answers
4k
views
Edit FASTA header using sed
I need to rename the following headers from a FASTA file. Something like:
...
- 21
1
vote
2
answers
2k
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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 ...
- 113
1
vote
2
answers
62
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 ...
- 1,797
1
vote
2
answers
39
views
Print first colum is the condition is true using awk
I have a binary file which looks like this,
...
- 23
1
vote
2
answers
178
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:
...
- 153
1
vote
1
answer
79
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...
- 127
1
vote
1
answer
54
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 ...
- 63
1
vote
1
answer
126
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 ...
1
vote
1
answer
76
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 ...
- 81
1
vote
1
answer
257
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 ...
- 11
1
vote
1
answer
49
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 ...
- 19
1
vote
3
answers
820
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
...
- 11
1
vote
1
answer
121
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?
...
- 331
1
vote
1
answer
33
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 ...
1
vote
1
answer
46
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:
...
- 129
1
vote
3
answers
148
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 ...
- 21
1
vote
1
answer
43
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 ...
- 121
1
vote
2
answers
558
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 ...
- 29
1
vote
1
answer
1k
views
1
vote
1
answer
463
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:
...
- 2,449
1
vote
0
answers
134
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 ...
- 836
1
vote
1
answer
629
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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 ...
- 836
1
vote
0
answers
259
views
tmhmm installation and running
I am trying to predict transmembrane protein using tmhmm-2.0c. According to Package instruction, I have changed the path of perl inside the program like as ...
1
vote
0
answers
387
views
TBLASTN error: Too many positional arguments
I was running tblastn using standalone blast2.9.0+ through Ubuntu Linux, to get the alignment result of a list of protein sequences for same species, against its complete genome file.
The command I ...
- 11
1
vote
1
answer
45
views
Installing Rostlab's PredictProtein
I am trying to install Rostlab's PredictProtein in a Virtual Machine as detailed here https://rostlab.org/owiki/index.php/How_to_Run_The_PredictProtein_Machine_Image_with_VirtualBox:
Download ...
- 113
0
votes
2
answers
170
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 ...
- 1,797