Questions tagged [linux]
The linux tag has no usage guidance.
47
questions
0
votes
1answer
27 views
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 ...
0
votes
2answers
50 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.
...
0
votes
1answer
86 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?
...
0
votes
2answers
44 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:
...
1
vote
1answer
32 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 ...
1
vote
2answers
49 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:
...
1
vote
1answer
36 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...
1
vote
3answers
74 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 ...
-1
votes
1answer
103 views
1
vote
1answer
58 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?
...
5
votes
3answers
498 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:
...
2
votes
2answers
98 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 ...
1
vote
1answer
36 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 ...
-1
votes
1answer
27 views
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 ...
2
votes
4answers
125 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/) ...
1
vote
4answers
2k views
Edit FASTA header using sed
I need to rename the following headers from a FASTA file. Something like:
...
0
votes
1answer
408 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 ...
1
vote
2answers
1k 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 ...
0
votes
1answer
550 views
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 ...
2
votes
2answers
56 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 ...
0
votes
2answers
124 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 ...
0
votes
2answers
117 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
vote
0answers
82 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 ...
0
votes
2answers
90 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 ...
1
vote
2answers
129 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 ...
0
votes
1answer
386 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?
1
vote
4answers
940 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 ...
0
votes
1answer
37 views
Replacing some strings in R or terminal
I have a .txt file; I have 139 unique sample IDs in sampleID column
...
8
votes
5answers
7k views
How to download FASTA sequences from NCBI using the terminal?
I have following accession numbers of the 10 chromosomes of Theobroma cacao genome.
...
2
votes
1answer
162 views
"perl: warning: Setting locale failed." in RepeatMasker
I'm trying to run Repeatmasker in Linux on the command line with:
...
1
vote
2answers
401 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 ...
3
votes
2answers
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.
...
1
vote
1answer
759 views
3
votes
4answers
1k 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 ...
3
votes
2answers
611 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:
...
5
votes
3answers
960 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.
3
votes
3answers
98 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.
...
2
votes
1answer
521 views
-1
votes
2answers
558 views
Script to run everything in a loop for extracting tar.gz files into fastq and to bam with alignment?
Original tar.gz files look like below:
...
1
vote
1answer
44 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 ...
0
votes
1answer
345 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:
...
-1
votes
1answer
298 views
Unable to Install PGDSpider using Ubuntu and wine
I'm running wine v 2.0.3 using ubuntu v. 16.04.2 on a Mac. I'm trying to install a program called PGDSpider2 from here. Essentially the program is supposed to convert different file formats used for ...
3
votes
0answers
207 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:
...
8
votes
7answers
1k 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.
3
votes
1answer
413 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-...
9
votes
5answers
950 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 ...
6
votes
2answers
381 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?
...
