Shortbred returns all zero count

Microbial community profiling ShortBRED
1

Dear shortbred developers,

Good morning!

Thank you for the fantastic bioinformatics tool! Recently I met a issue, which bother me for a long time, I hope I can get some issue or idea from you.

I need to map metatranscriptomic data(where readlength is 50bp) against certain family of proteins( OXC,OXDD,FRC). But somehow, results didn’t return any count or hit except 0. And I tried parameter —pctlength from 0.1 to 0.9, and id from 0.1 to 0.9. But all failed. Besides, diamond blast indicates three protein families indeed exists there. And another metagenomic data(150bp) works well with shortbred. So I don’t think it is code issues.

Reference dataset is uniref 90.
Proteins of interest are from interpro.

Any help and suggestions will be greatly appreciated!

Ze Chen

2

ShortBRED uses an internal minimum-read-length filter (--minreadBP) that defaults to 90 nt. You can lower this value to generate more alignments from the shorter reads you’re using. Sorry for the delayed reply - let us know if this helps?