Questions tagged [bash]

Use this tag to refer to the questions related to the Linux and Unix shell abbreviated as bash (Bourne Again SHell). It has notable programmatic strengths over C shell (csh) and touch C shell (tcsh)

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Cannot blast against specific NCBI databases

I am having issues with some prokaryote reference genome databases (exact names : ref_prok_rep_genomes.*), that I downloaded from the NCBI website : https://ftp.ncbi.nlm.nih.gov/blast/db/. Files in ...
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25 views

How to calculate GenePy score for vcf files in all subdirectories?

In a parent directory, I have several sub-directories, each of them contain one .vcf.gz file on which analysis should be performed. I want to run following commands on all .vcf.gz files in all ...
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1answer
30 views

Table error when combining counts columns

I have these files that I want to make table of (https://github.com/learnseq/RNAseqfiles01.git), the table that I want (since all the files have the same ID column),, I want merge the ID column with ...
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27 views

Issues with AutoDock Vina

I am trying to use AutoDock Vina to do docking however I am getting this error. I would really appreciate any help as I have not been able to resolve this error despite trying numerous times.
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0answers
23 views

Command-line blastn not responding; trace says “Resource not available”

I hadn't used the NCBI command-line tools for a while, and just got back into it. But no matter where or how I run blastn now, I get an almost complete lack of response: just the initial "BLASTN ...
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47 views

Changing alpha-numeric IDs to numeric only IDs

I need to convert my three text files to the exact formatting of the corresponding example files in order to run my code. I think the formatting error being generated is from the geneID (bold) ...
0
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1answer
61 views

How to use extractfeat?

I am working on a script on bash linux to get the CDS (coding sequence) of a gene using extractfeat by EMBOSS. It gives me the error: Warning: No sequences written to output file I am unsure if my ...