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3 votes
1 answer
37 views

Passing data from the Agilent Trimmer utility to bwa-mem2 via a named pipe

I am trying to use a named pipe to pass data from the Trimmer utility from the AGeNT toolbox from Agilent, through bwa-mem2. The normal behavior is that the Trimmer utility writes trimmed fastq files ...
3 votes
1 answer
362 views

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

I'm trying to run Repeatmasker in Linux on the command line with: ...
0 votes
1 answer
122 views

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 ...
1 vote
2 answers
98 views

How to parse hmmsearch output?

I did hmmsearch with --notextw and --domtblout and I see several results for ids, I want to ...
1 vote
1 answer
39 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 - ...
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. ...
2 votes
1 answer
63 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 ...
-1 votes
1 answer
79 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 ...
3 votes
2 answers
853 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: ...
1 vote
1 answer
152 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 ...
0 votes
0 answers
33 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?
3 votes
1 answer
97 views

Extract specific nucleotide base position for query and subject from text file

I have an input file looks like this: ...
0 votes
1 answer
75 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 ...
4 votes
3 answers
327 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(...
-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 ...
1 vote
1 answer
716 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 ...
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 ...
1 vote
1 answer
71 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: ...
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 ...
0 votes
2 answers
198 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 ...
0 votes
1 answer
997 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? ...
2 votes
3 answers
205 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: ...
1 vote
1 answer
112 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 ...
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 ...
0 votes
1 answer
348 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 ...
0 votes
0 answers
138 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?
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 ...
1 vote
1 answer
532 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 ...
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 ...
3 votes
1 answer
241 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: ...
1 vote
1 answer
62 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 ...
1 vote
0 answers
196 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 ...
1 vote
0 answers
427 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
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 ...
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, ...
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 ...
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 ...
0 votes
1 answer
135 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
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. ...
0 votes
2 answers
506 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
1 answer
76 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
2 answers
240 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
1 answer
109 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...
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 ...
1 vote
3 answers
228 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 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 ...
5 votes
3 answers
3k 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: ...
0 votes
1 answer
1k views

Cellranger gives error

I am trying to run cellranger but I get fastq permission denied error ...
1 vote
1 answer
207 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? ...
3 votes
2 answers
683 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 ...