how to create an interval file to extract sequences?

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3.0 years ago

crissavega23 • 0

Hi! I am trying to create a interval file to extract sequences that is needed to use bedtools, the thing is that I run a blast nad filtered the results, so now I have a fasta file with the ID of the query protein, the subject protein and the location of those secuenques in the proteome, but I don´t know how to create the file that bedtools needs to extract sequences with the "getfasta" tool.

Thanks!

bedtools sequences blast fasta • 699 views

ADD COMMENT • link updated 3.0 years ago by GenoMax 141k • written 3.0 years ago by crissavega23 • 0

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Interval file can be in BED format with min 3 columns.

chr/ID         start        stop

That said if you are trying to retrieve protein sequences then I am not sure if bedtools getfasta will work.

There are some options in this thread: How to extract a peptide sequence (interval) from a FASTA file?

ADD REPLY • link 3.0 years ago by GenoMax 141k

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