doubts about SNAP, bioinformatic tools for gene prediction

Question

[JUAN LUIS]

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.

I thank you all in advance for reading and helping me.

Best regards!

Juanlu

[lieven.sterck]

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!