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Questions tagged [bash]

Use this tag to refer to the questions related to the Linux and Unix shell abbreviated as bash (Bourne Again SHell).

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2 answers
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How to add corresponding "chr" before location (start, end) of bed alike file?

I have some bed alike files but don't have chr term in the fisrt column, that I want to add chr and its corresponding chromosome ...
Deb's user avatar
  • 211
0 votes
1 answer
112 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 ...
Zizogolu's user avatar
  • 2,148
1 vote
1 answer
18 views

Salmon Multiple File SCRIPT giving error

Hi I am using Salmon quantitation for multiple fastq paired files using following code ...
Malik Saad's user avatar
1 vote
0 answers
54 views

tabix to subset each VCF by the coordinates given

I have a vcf file like below ...
Zizogolu's user avatar
  • 2,148
3 votes
2 answers
125 views

Printing the results of for loop into a txt file

I have a for loop which prints available vcf files in the path for a list of patient IDs (using find dx data function) into my zsh terminal: ...
Zizogolu's user avatar
  • 2,148
-1 votes
1 answer
26 views

Concatenate multiple fasta files into individual files per unique entry

I have several splitted fasta files like this: TK273759.fastaaa TK273759.fastaab TK273759.fastaac TK273759.fastaad TK273759.fastaae I want to concatenate these ...
Sufia Akter Neha's user avatar
-2 votes
3 answers
84 views

Filtering columns from large file based on a column list

I have list of samples as a txt file and want to only keep these samples from this large file; column name is samples name in the large file. ...
bioinfonext's user avatar
2 votes
0 answers
51 views

Racon: empty overlap set!

Not sure if anyone can help me with a Racon issue as the developers are not very responsive on GitHub. I am trying to assemble a genome without a reference. I first did basecalling using dorado, then ...
Setshaba's user avatar
0 votes
2 answers
84 views

How to calculate average from a column when consecutive cells are similar in different columns?

I wonder how can I calculate the average of column 7 (WPS_win) when consecutive cells in column 2, column 3, and column 1 are the same. The file is in bed format (tab-separated format). The original ...
Deb's user avatar
  • 211
0 votes
0 answers
76 views

Old program make error ProtDeform

Im trying to run ProtDeform on ubuntu 20.04 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125161/ I need scoring function :/ to my project But error occurs: ...
MTG's user avatar
  • 147
2 votes
1 answer
120 views

Analysis of RNA sequencing with zUMIs

I wrote the .yaml file which was according the instruction from zUMIs: ...
Isidora Pantovic's user avatar
0 votes
1 answer
111 views

A bash script for running on a bunch of bam files

I have some bam files in this directory /data/Continuum/WES/results/ I want to run GATK mutation calling over bam files I ...
Zizogolu's user avatar
  • 2,148
1 vote
1 answer
50 views

Create bam from separate sam and header

If I have multiple SAM files without header, and a header saved in a separate file, how do I convert that to a BAM file? One solution is to create intermediate files: ...
Alexlok's user avatar
  • 384
4 votes
2 answers
205 views

How can I give different names to files in a directory with a for loop in a bash script?

I'm expecting to get 17 different paired-end fastq files (34 in total), so I want to make a bash script to just run my code through all the fastq files in a directory at once. How can I change the ...
Pablo O. García Díaz's user avatar
0 votes
1 answer
50 views

How can I change all text in a .tsv file to 1, except the first three fields?

I want to convert a .tsv file table in binary format (1 and 0). In which all cells containing text would become 1 and blank cells would become ...
Deb's user avatar
  • 211
1 vote
3 answers
255 views

How to join multiple large .tsv (> 20 GB, bed file) files by two identifier?

This question has also been asked on Biostars I wonder how can I join multiple large .tsv files (over 20 GB each) by using two identifiers (columns) which I used to do using the ...
Deb's user avatar
  • 211
0 votes
1 answer
29 views

Variant Filtering Using AnthonyOzerov/variant-filtering Github Repository And Python Errors

I am using the following Github repository that I cloned. One apparent issue is that it is using an old/defunct link for the phenotype_to_genes.txt that is no longer active and after several tries I ...
Indira's user avatar
  • 380
1 vote
2 answers
197 views

Singularity And CNV Kit

I would like to try an use Singularity with CNV kit as the HPC I use seems to work better with Singularity: Initial Attempt: ...
Indira's user avatar
  • 380
2 votes
1 answer
91 views

CNV Kit ` from . import commands ImportError: cannot import name 'commands' from '__main__'`

I am trying to run some code for my colleague in bash ...
Indira's user avatar
  • 380
3 votes
3 answers
348 views

Easier / lazy way to convert an existing bash pipeline to nextflow pipeline?

Not going to lie, my head hurts when I read the NextFlow documentation (No dig on the documentation, I think my head is losing its processing capacity lol). I had written a pipeline in Bash, ...
Karthik Nair's user avatar
2 votes
4 answers
661 views

Parallelize or qsub a bash script

I have a bash script that I would like to parellelize to run on multiple nodes. My goal is to run my python sample_script.py script on pairwise comparisons of samples to see if their variants are a ...
che625's user avatar
  • 21
2 votes
1 answer
109 views

Dealing With Manta Limitations

I am trying to figure out a way to remove the limiting factors that Manta says it cannot handle. To quote from the Manta page: The following limitations exist on the input BAM or CRAM files provided ...
Indira's user avatar
  • 380
3 votes
1 answer
44 views

Passing strings for password, email authentication and download link

Hi I am downloading the data from a website which requires authentication of email_id and password before the download. They then provide the download link which is used to download dataset. This ...
Priya's user avatar
  • 351
2 votes
1 answer
104 views

Manta "--exome: command not found"

I am using Manta (https://github.com/Illumina/manta/blob/master/docs/userGuide/README.md) but whenever I try to specify the --exome command using the following code ...
Indira's user avatar
  • 380
0 votes
1 answer
72 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
2 votes
1 answer
84 views

Default placeholder for missing fields doesn't work with block in xtract tool

I am using the xtract tool of the Entrez Direct (EDirect) package of NBCI. I have a list of Accession Numbers: ...
Rossy Clair's user avatar
1 vote
4 answers
192 views

How to remove empty files from a directory?

I have a directory of FASTA files, some of which are empty (placeholders that were output from a pipeline) and I would like to delete the empty files using a for loop on the command line. From what I ...
rimo's user avatar
  • 963
5 votes
4 answers
502 views

How to rename a file based on a directory name?

I have a lot of FASTA files that I recently scaffolded with RagTag. The output of RagTag includes a directory for each sample and the corresponding FASTA file written as "ragtag.scaffold.fasta&...
rimo's user avatar
  • 963
3 votes
1 answer
291 views

Run nextflow pipeline multiple times depending on length of a list

This question was also asked on Stack Overflow I have a Nextflow pipeline that runs a BUSCO search on input data, returns the output and then creates a report based on the output. One of my parameters ...
CornOnTheCob's user avatar
1 vote
1 answer
57 views

Problems with BED format for ClinCNV

I have some problems with ClinCNV(https://github.com/imgag/ClinCNV): I made a BED file from a BAM, then i made a GC count with ngs-bits (link: https://github.com/imgag/ngs-bits ) The main idea of ...
Илья Бетяев's user avatar
3 votes
1 answer
120 views

How to remove double '/' from file path, bash script

I'm using the following script to detect strandedness of my paired end RNA-seq data. ...
pubsurfted's user avatar
2 votes
2 answers
861 views

How to wget a gff from NCBI database?

Say I want to use wget to download a gff file for the X chromosome of release 5.57 of the Drosophila melanogaster genome. The NCBI page with the gff file for just this is here. However, I do not see ...
arara's user avatar
  • 152
1 vote
3 answers
90 views

eQTL data extraction from database JSON file

I have a long list of JSON data, with repeats of contents similar to followings. Due to the original JSON file is too long, I will just shared the hyperlinks here. This is a result generated from a ...
austin7923's user avatar
2 votes
1 answer
115 views

Error Registering Job Definition AWS

I am in the process of creating a bioinformatics pipeline and I am currently trying to setup the AWS infrastructure for which it will run. The script I am running to setup the AWS batch job looks like ...
Joe_G's user avatar
  • 101
1 vote
2 answers
165 views

Is there an equivalent of Entrez queries for local BLAST?

I have been having some trouble with running command line BLASTn remotely. Therefore, upon recommendations, and considering I have >100 searches planned, I am considering just downloading the nt ...
Laura's user avatar
  • 909
1 vote
1 answer
182 views

Running a Python Script from a bash script on multiple input files across different directory paths

I am in the process of writing up a bash script that runs three bioinformatics tools and then executes a python script. This python script compiles some of the data from the informatics tools output ...
Joe_G's user avatar
  • 101
3 votes
2 answers
422 views

Remote blastn - what is breaking my (bash) loop?

I am trying to search the NCBI non-redundant database for sequences similar to a few other (~40) sequences that I already have. So I've tried running blastn remotely, and looping through multiple ...
Laura's user avatar
  • 909
4 votes
0 answers
132 views

Write a bash script to run gatk, fix errors with input, and rerun until completion

I have a bam file that I want to run through GATK's SplitNCigarReads tool. Because of the way the bam file was generated, the program will often fail, with an error message stating: ...
kylep's user avatar
  • 41
3 votes
2 answers
92 views

bash script for interproscan REST

hey i have the problem with bash script. It should run interproscan REST Im green in bash scripting. I found this script on the web: ...
MTG's user avatar
  • 147
2 votes
0 answers
53 views

Is there a way antiSMASH can be used to screen a large number of genomes just for one type of biosynthetic gene cluster?

When we use antismash command with the genome sequence file as follows: antismash GCA_002095535.1_ASM209553v1_genomic.gbff it screens the genome for all the ...
snap_v's user avatar
  • 21
3 votes
4 answers
964 views

How can I add a ";" at the end of each fasta header line in a file?

I have a large fasta file with RNA sequences. I need to add a ; at the end of each header line (lines beginning with >) in ...
Callahan McGovern's user avatar
2 votes
1 answer
837 views

How do I use bash for loops to loop through a WDL Array?

Within the example below a WDL array of strings, test is defined as "a","b","c","d" the ...
Logios James's user avatar
2 votes
2 answers
152 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
2 votes
1 answer
259 views

Python argparse error

Hi I am trying to use this python script (running with bash script) to do my analysis. I am getting the following error: File "my_python_script.py", line 33 logging.info("Reading input2 ...
Riya's user avatar
  • 307
1 vote
2 answers
291 views

Permutations of 4 amino acid sequence oligopeptide

I have an assignment for a project to build a tetrapeptides library to screen against some target enzymes in silicon. I am looking for a script to construct about 160000 tetrapeptide from the 20Amino ...
Ruthy's user avatar
  • 11
0 votes
1 answer
13k views

curl: (22) The requested URL returned error: 400 Bad Request when using entrez direct

I've just dowloaded entrez direct on my Mac and I was trying to perform some simple queries like: ...
Mario Cat's user avatar
1 vote
2 answers
80 views

Is there a way to calculate the Ka/Ks value in R/unix?

I am investigating the rate of synonymous non synonymous substitutions and would like to find the Ka/Ks value also known as dn and ds between multiple alleles? I want to investigate multiple alleles ...
mk894's user avatar
  • 105
2 votes
1 answer
43 views

Automatize classical debugging in a bash script? (normal debugging by hand)

And thanks in advance. I am debugging a text file which is the one the two inputs on the program RGmatch https://bitbucket.org/pfurio/rgmatch/src/master/. The code works. Is that some records give ...
Edmond Geraud Aguilar's user avatar
1 vote
2 answers
432 views

Retain only part of a file name and fasta header in fasta directory

I have a MainDirectory/hundreds_of_subdirectories/thousands_of_fastas structure. For each fasta in the bottom level, I am trying to change the file name as well as ...
Malia W's user avatar
  • 21
1 vote
0 answers
21 views

Nucleotide Frequency - HOMER?

I'm trying to find the frequency of UA dinucleotide in a bed file. I want to convert the bed file to FASTA, count all the UA dinucleotides up, then divide by the total length of the FASTA file. Also, ...
Kyle Stangline's user avatar