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How to know if FASTQ/BAM is from reference genome (FASTA)?

In general, this answer wouldn't be more correct than @Ram RS' answer but here is how I would approach: I would start everything from scratch, at the end of the day you will most probably need to ...
haci's user avatar
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2 votes

How to know if FASTQ/BAM is from reference genome (FASTA)?

Your post has multiple questions but one of them is not really a question so I'll address everything here: 1. "Some of them could be contaminants, so I'd like to filter them out and get only the ...
Ram RS's user avatar
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0 votes

Salmon Multiple File SCRIPT giving error

Are you sure the find operations return exactly one file each? The error seems to state that there were no files found for some run. Or it could also be that you ...
Ram RS's user avatar
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2 votes
Accepted

Finding homologous regions in multiple whole genomes

According to show cords the format you are getting contains columns which you can use to obtain BED format with relevant information. You need following columns: <...
darked89's user avatar
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4 votes
Accepted

split fastq file containing a sequence block at different locations

You can try seqkit locate with say start or end of CDS sequence. This will give you a tabulated output with locations of your CDS query in each read. Since you expect that the CDS sequence should be ...
darked89's user avatar
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