Questions tagged [linux]
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73
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2
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1
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59
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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
43
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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
...
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1
vote
1
answer
62
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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 ...
- 53
0
votes
0
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29
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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?
- 53
3
votes
1
answer
77
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Extract specific nucleotide base position for query and subject from text file
I have an input file looks like this:
...
- 31
0
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1
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55
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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 ...
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4
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3
answers
303
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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(...
- 81
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1
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133
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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 ...
- 81
1
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1
answer
294
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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 ...
4
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4
answers
673
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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 ...
- 115
1
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1
answer
56
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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:
...
- 159
0
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2
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128
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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 ...
- 1
0
votes
2
answers
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 ...
- 1
2
votes
3
answers
116
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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:
...
- 361
0
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0
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97
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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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2
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2
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130
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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 ...
- 21
0
votes
1
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248
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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 ...
- 435
1
vote
1
answer
85
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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 ...
- 91
1
vote
1
answer
348
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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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1
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1
answer
59
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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 ...
- 19
1
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0
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155
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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 ...
- 836
1
vote
1
answer
785
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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 ...
- 836
1
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2
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40
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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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1
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0
answers
309
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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 ...
1
vote
3
answers
972
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
...
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3
votes
3
answers
81
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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
...
- 41
0
votes
1
answer
116
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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 ...
- 41
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2
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809
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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.
...
0
votes
1
answer
818
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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?
...
- 1
0
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2
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379
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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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1
vote
1
answer
64
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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 ...
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1
vote
2
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190
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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:
...
- 153
1
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1
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89
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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...
- 127
1
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3
answers
170
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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 ...
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1
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854
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Cellranger gives error
I am trying to run cellranger but I get fastq permission denied error
...
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1
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1
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157
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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?
...
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5
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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:
...
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2
answers
479
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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 ...
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1
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1
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44
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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 ...
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1
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35
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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 ...
2
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4
answers
426
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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/) ...
1
vote
4
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4k
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Edit FASTA header using sed
I need to rename the following headers from a FASTA file. Something like:
...
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0
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1
answer
1k
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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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1
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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 ...
- 113
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1
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1k
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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 ...
- 109
1
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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 ...
- 1,951
0
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2
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196
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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 ...
- 1,951
0
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2
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174
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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 ...
- 1,951
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0
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439
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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 ...
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2
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124
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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 ...
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