doubts about SNAP, bioinformatic tools for gene prediction
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7 weeks ago
JUAN LUIS • 0

Hello to all

I am using snap software to perform gene prediction. I have already generated the necessary .hmm database, and now I want to run it. I have run it as follows:

snap db.hmm assembly.fasta -gff -aa -tx -name <species>


However, after running it, no output gff file has been generated, despite giving it the '-gff' option as input.

I know that by default, snap generates a file in zff format, in fact, I have tried running it like this 'snap db.hmm assembly.fasta', and it does generate an output in zff format. However, when I use the zff to gff3 conversion script that the snap developers have uploaded on github, this script does not do the conversion well, so it generates a defective gff file that I can not load in igv.

Does anyone know why the -gff option does not generate the output file in .gff format ? On the other hand, do you know any script that allows me to convert the output zff file to a gff3 format to be able to visualize it in IGV ? I could either generate the output gff3 document directly by snap, or a script that allows me to convert the zff to gff3 correctly.

Best regards!

Juanlu

gene prediction • 157 views
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Entering edit mode

Hello JUAN LUIS,

Welcome to the forum!

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

Thank you!