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How to debug a bash script

Please somebody debug my code In sub-folders there are 500000 vcf files from which I only need 500 vcf files listed in ...
Zizogolu's user avatar
  • 2,160
1 vote
2 answers
81 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
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
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
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
-1 votes
1 answer
77 views

stats.sh error in BBmap package

I am trying to calculate the N50 value from the assembled FASTA file. I used stats.sh from the BBmap package. I executed the following command ...
seq's user avatar
  • 9
1 vote
1 answer
143 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
0 votes
0 answers
32 views

How to access specific SRA sequences within an SRP file?

How do you get a specific 100 SRA sequences from a Bioproject which contains 400 runs, when you don't need all of them?
K_081's user avatar
  • 149
3 votes
1 answer
95 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
0 votes
1 answer
73 views

Replace a string in a column of a text file based on matching string listed in another file using linux

I have multiple sets of files, so I grepped the list from a column in a seperate file such as file1.txt. I want to change all other files by using this file1.txt based on a matching string. for ...
Umar's user avatar
  • 135
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
-1 votes
1 answer
137 views

computing the distance between ( XYZ coordinates)

I have a txt file (50k) proteins in it, which looks like this: line 1:the protein code line 2: protein length in amino acids line 3: amino acid sequence line 4: secondary structure line 5: XYZ ...
Amal's user avatar
  • 81
1 vote
1 answer
655 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
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
1 vote
1 answer
69 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
0 votes
2 answers
188 views

How to find restriction enzyme frequency in whole genome and count the distance between them?

I am having possibly a simple question which is proving difficult. My objective is to take the reference FASTA file and flat file database with 1500 restriction enzymes with its cutting sites (mostly ...
Santosh's user avatar
0 votes
2 answers
32 views

Assemble Anaeroplasma species genome from metagenomic PacBio data

I have a fasta file containing reads generated by PacBio HiFi whole genome sequencing of a feces sample from mouse. I would like to use this dataset to generate an assembled circularized genome for an ...
Amroon's user avatar
  • 1
2 votes
3 answers
190 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
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0 votes
0 answers
132 views

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?
K.Harini'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
0 votes
1 answer
340 views

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 ...
Vovin's user avatar
  • 435
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
517 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
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
  • 836
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
  • 836
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
0 answers
418 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 ...
Kishor Kumar Sarker's user avatar
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
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
0 votes
1 answer
133 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 ...
Justin1609's user avatar
0 votes
2 answers
1k 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. ...
Michelle Yang's user avatar
0 votes
1 answer
973 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? ...
Greater's user avatar
0 votes
2 answers
485 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: ...
MicroBiostat's user avatar
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
2 answers
233 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
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
0 votes
1 answer
1k views

Cellranger gives error

I am trying to run cellranger but I get fastq permission denied error ...
Zizogolu's user avatar
  • 2,160
1 vote
1 answer
201 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
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
3 votes
2 answers
667 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
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 votes
1 answer
46 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 ...
Nargis Naqvi's user avatar
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
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
0 votes
1 answer
1k 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 ...
Brian's user avatar
  • 11
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
0 votes
1 answer
2k 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 ...
Kumar's user avatar
  • 109
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