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TravisWheelerLab / BATH

Better Alignments with Translated HMMER
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Output format #5

Closed xvtyzn closed 7 months ago

xvtyzn commented 8 months ago

Dear BATH developers,

I sincerely thank you for developing such an excellent tool.

I have a question about the BATH output format. As bash follows a kind of hmmer, I think the result file is hmm format. However, I would like to see the results in gff format in order to utilise it for gene prediction based on robust features such as frameshift.

Do you plan to increase the number of output formats or do you know anything about how to convert them?

Best regards,

Keigo

GenevieveKrause commented 8 months ago

Hello,

BATH uses HMMs as input files or the protein query. The output is the set of alignments for all the hits between those queries and the DNA target sequences. You can also request a tabular version of all the hits using the '--tblout' flag. There are no plans to produce a gff format output but you should be able to convert the tabular output to a gff file with a simple post-processing script.