Problem when converting from blast output table to GTF file.

Question

[v.berriosfarias]

Hello, from an alignment of genes against metagneomic contigs using mmseqs2 I got a blast output format 6 table.

For the purpose of performing a gene abundance calculation from the metagenomes I want to use htseq program.

for htseqI need as input bam files (which I have) and gif files. The issue is that when I convert the blast tables (with .m8 extension) to off using blast2gff program (https://github.com/wrf/genomeGTFtools/blob/master/blast2gff.py) I got the following table:

From that table I used gffread on te next way:

gffread file.gff3 -T -o file.gtf

but the resulting table is an empty one.

What is the best way of converting off table or blast table (outfmt 6) to a gif file?

Thanks for your time :)

Answer 1

[Juke34]

I guess gffread does not deal with match_part feature type (3rd column of your GFF file.) You should use agat_convert_sp_gff2gtf.pl from AGAT with option "Relax".

[v.berriosfarias]

Thank you so much!! it reduced my anxiety