Questions tagged [linux]

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Locate the saved template of minknow

I am using minknow on ubuntu. After saving the template (settings), where is that file locally stored in the system? Also what is its format/extension?
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2 votes
2 answers
52 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 ...
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1 answer
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BEAGLE do not see and/or not use OpenCL

I am conducting phylogeny analyses using BEAST 2 as software tool. It is said that it can be accelerated by BEAGLE-library. I have a personal laptop with Windows & a cluster with CentOS. I ...
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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 ...
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1 answer
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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 ...
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1 vote
1 answer
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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 ...
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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 ...
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1 answer
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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 ...
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2 answers
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Print first colum is the condition is true using awk

I have a binary file which looks like this, ...
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0 answers
78 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 ...
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2 answers
223 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 ...
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3 votes
3 answers
64 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 ...
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1 answer
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Error when using awk command to trim sequence files

I am attempting to edit my fastq sequence files with an awk command from a published article. The sequence files are all ...
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2 answers
160 views

Using grep to get lines from a file (.tsv) that contain specific samples listed in a sample file (.tsv)

So I have a file, let's call it pcawg.tsv. It's formatted like the one down below. ...
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1 answer
316 views

Converting Fastq files to Fasta files on Ubuntu

I am new to bioinformatics and programming. I tried to convert my fastq files to fasta file, but got this. What could be wrong? ...
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2 answers
91 views

Remove from Multi-FASTA by Sequence ID

I want to remove sequence VRE32514 – it doesn’t belong and thus is the reason it lacks additional metadata. However I tried implementing this code from a similar question: ...
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1 vote
1 answer
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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 ...
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1 vote
2 answers
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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: ...
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1 vote
1 answer
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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...
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3 answers
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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 ...
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-1 votes
1 answer
280 views

Cellranger gives error

I am trying to run cellranger but I get fastq permission denied error ...
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1 vote
1 answer
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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? ...
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5 votes
3 answers
997 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: ...
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2 votes
2 answers
152 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 ...
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1 vote
1 answer
37 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 ...
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-1 votes
1 answer
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DNA seq cutting using Linux [closed]

I need to use the cut command on a human insulin sequence row wise but i don't know the command.I already ran byte wise command but the gave me column wise results. I cant use the -f option since i ...
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2 votes
4 answers
216 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/) ...
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2 votes
4 answers
3k views

Edit FASTA header using sed

I need to rename the following headers from a FASTA file. Something like: ...
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1 answer
607 views

VCF-merge fails due to tabix not producing .tbi files

I'm trying to use vcf-merge to combine 2 exome capture vcf files (~250K and ~330K in size) before trying it on all 96 samples. I'd appreciate any advice on the best way to do that! I've detailed what ...
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2 answers
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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 ...
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1 answer
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How to generate ultrametric phylogenetic trees?

This question has also been asked on Biostars I am going to use ultrametric tree for downstream analysis. I would like to see use the ultrametric tree for Ranger-DTL for infer gene family evolution by ...
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2 votes
2 answers
60 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 ...
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  • 1,513
0 votes
2 answers
138 views

Looping over several files in bash

I have a bash script: I am wondering how I can change this script to loop over a bunch of .vcf files and give output .txt with the name of corresponding .vcf I tried changes done in similar script ...
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  • 1,513
0 votes
2 answers
132 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 ...
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1 vote
0 answers
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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 ...
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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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1 vote
2 answers
133 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 ...
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0 votes
1 answer
553 views

How to convert mzXML to mzML format (mass spectrometry files)?

How to convert mzXML to mzML format (mass spectrometry files) preferably under Linux and/or Python?
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1 vote
4 answers
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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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0 votes
1 answer
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Replacing some strings in R or terminal

I have a .txt file; I have 139 unique sample IDs in sampleID column ...
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9 votes
5 answers
11k views

How to download FASTA sequences from NCBI using the terminal?

I have following accession numbers of the 10 chromosomes of Theobroma cacao genome. ...
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2 votes
1 answer
238 views

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

I'm trying to run Repeatmasker in Linux on the command line with: ...
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1 vote
2 answers
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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 ...
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3 votes
2 answers
2k 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. ...
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1 vote
1 answer
962 views

Error in installing Vep

I am trying to installing Vep on Linux but an error is permanent ...
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  • 1,513
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 ...
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3 votes
2 answers
669 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: ...
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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.
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3 votes
3 answers
112 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. ...
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2 votes
1 answer
650 views

How do I filter a GFF file by gene type?

I have a file with following information: ...
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