Filter gmap GFF3 output by identity

Question

[karthic]

Hi,

I have aligned my coding sequences to the genome using gmap with output format as as --gff3-match-cdna. Now I want to filter this gff3 to keep only the records having more than 90% identity.

How can i do that??

Thanks, Karthic

Answer 1

[Juke34]

If the identity is stored in an attribute of the 9th column you can filter using agat_sp_filter_feature_by_attribute_value.pl from AGAT

[karthic]

Thanks for your quick reply.My gff3 has an attibute "gap" which has cigar like values. Below are the few lines...

HiC_scaffold_4901       gmapk15_genomeIndex     cDNA_match      38678   39960   99      -       .       ID=Gills_HQ_transcript/28860.path1;Name=Gills_HQ_transcript/28860;Dir=indeterminate;Target=Gills_HQ_transcript/28860 1 1282;Gap=M500 D1 M782
###
HiC_scaffold_2006       gmapk15_genomeIndex     cDNA_match      47241   47314   98      +       .       ID=Gills_HQ_transcript/30236.path1;Name=Gills_HQ_transcript/30236;Dir=sense;Target=Gills_HQ_transcript/30236 2 75;Gap=M74
HiC_scaffold_2006       gmapk15_genomeIndex     cDNA_match      49296   49564   100     +       .       ID=Gills_HQ_transcript/30236.path1;Name=Gills_HQ_transcript/30236;Dir=sense;Target=Gills_HQ_transcript/30236 76 344;Gap=M269
HiC_scaffold_2006       gmapk15_genomeIndex     cDNA_match      49853   50656   99      +       .       ID=Gills_HQ_transcript/30236.path1;Name=Gills_HQ_transcript/30236;Dir=sense;Target=Gills_HQ_transcript/30236 345 1148;Gap=M804
###
HiC_scaffold_5615       gmapk15_genomeIndex     cDNA_match      4336    6256    99      +       .       ID=Gills_HQ_transcript/4125.path1;Name=Gills_HQ_transcript/4125;Dir=sense;Target=Gills_HQ_transcript/4125 1 1919;Gap=M23 D1 M192 D1 M1704
HiC_scaffold_5615       gmapk15_genomeIndex     cDNA_match      6455    6580    100     +       .       ID=Gills_HQ_transcript/4125.path1;Name=Gills_HQ_transcript/4125;Dir=sense;Target=Gills_HQ_transcript/4125 1920 2045;Gap=M126