Questions tagged [linux]
The linux tag has no usage guidance.
71
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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 ...
M__♦
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28
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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
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1
answer
319
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"perl: warning: Setting locale failed." in RepeatMasker
I'm trying to run Repeatmasker in Linux on the command line with:
...
CommunityBot
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3
votes
1
answer
68
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Extract specific nucleotide base position for query and subject from text file
I have an input file looks like this:
...
- 500
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50
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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 ...
- 2,706
4
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3
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292
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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(...
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129
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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 ...
- 500
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1
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126
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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 ...
- 13k
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4
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311
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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 ...
- 13k
1
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1
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46
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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:
...
- 13k
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3
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820
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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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- 377
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2
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98
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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 ...
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698
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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?
...
CommunityBot
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2
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3
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90
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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:
...
- 377
1
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1
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76
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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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31
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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 ...
- 6,295
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206
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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 ...
CommunityBot
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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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111
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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 ...
- 13k
1
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1
answer
257
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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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942
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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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228
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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:
...
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1
answer
49
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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 ...
CommunityBot
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0
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134
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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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0
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259
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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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1
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629
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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
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39
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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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3
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79
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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
...
- 755
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2
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2k
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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 ...
- 1,273
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1
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102
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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 ...
- 1,744
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2
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708
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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.
...
- 13k
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321
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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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54
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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 ...
- 1,744
1
vote
2
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178
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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
answer
79
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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...
- 9,352
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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 ...
- 13k
1
vote
3
answers
148
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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 ...
- 13k
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4
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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 ...
- 13k
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3
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2k
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Removing duplicate FASTA sequences based on headers with Bash
I used the following command to remove duplicate FASTA sequences based on the header sequence:
...
- 13k
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1
answer
713
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Cellranger gives error
I am trying to run cellranger but I get fastq permission denied error
...
- 13k
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1
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121
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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?
...
- 331
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2
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372
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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 ...
- 9,352
1
vote
1
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43
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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 ...
M__♦
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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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384
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How to make work programs from the $PATH?
I am trying to analyze my RNAseq reads for defective genomes and I use this program (http://www.di-tector.cyame.eu/) that is suggested by Beauclair et al (https://pubmed.ncbi.nlm.nih.gov/30012569/) ...
M__♦
- 10.2k
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4
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Edit FASTA header using sed
I need to rename the following headers from a FASTA file. Something like:
...
- 3,672
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118
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How I can run this code on my files?
I am annotating some .txt files by Annovar software by this code
nnovar]$ module load annovar/2016Feb01
[cyan01 annovar]$ table_annovar.pl
But I really got ...
- 3,672
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5
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18k
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How to download FASTA sequences from NCBI using the terminal?
I have following accession numbers of the 10 chromosomes of Theobroma cacao genome.
...
- 121
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2
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62
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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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2
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160
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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 ...
- 1,042