Questions tagged [linux]

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1
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2answers
26 views

Print first colum is the condition is true using awk

I have a binary file which looks like this, ...
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0answers
26 views

Calculating Polygenic risk scores using PRSICE 2 [closed]

I am trying to calculate PRS in UKBB individuals for a binary trait (T2D). For that I am using the PRSice 2 software, This is how my code looks like, ...
1
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0answers
24 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 ...
0
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2answers
80 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 ...
3
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3answers
55 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 ...
0
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1answer
37 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
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2answers
66 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
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1answer
143 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
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2answers
52 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
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1answer
35 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
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2answers
52 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
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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
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3answers
81 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
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1answer
151 views

Cellranger gives error

I am trying to run cellranger but I get fastq permission denied error ...
1
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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
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3answers
659 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
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2answers
110 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
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1answer
30 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
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4answers
137 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
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4answers
2k views

Edit FASTA header using sed

I need to rename the following headers from a FASTA file. Something like: ...
0
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1answer
460 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
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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
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1answer
651 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
57 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
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2answers
127 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
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2answers
121 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
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0answers
99 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
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2answers
100 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
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2answers
131 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
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1answer
439 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
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4answers
1k 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
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1answer
38 views

Replacing some strings in R or terminal

I have a .txt file; I have 139 unique sample IDs in sampleID column ...
9
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5answers
9k 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
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1answer
188 views

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

I'm trying to run Repeatmasker in Linux on the command line with: ...
1
vote
2answers
428 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
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1answer
797 views

Error in installing Vep

I am trying to installing Vep on Linux but an error is permanent ...
3
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4answers
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 ...
3
votes
2answers
638 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
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3answers
999 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
104 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
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1answer
559 views

How do I filter a GFF file by gene type?

I have a file with following information: ...
-1
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2answers
579 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
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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
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1answer
361 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
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1answer
308 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
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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
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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
416 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-...