Question: Filter gmap GFF3 output by identity
0
gravatar for karthic
29 days ago by
karthic100
karthic100 wrote:

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

gene prediction gmap genome • 95 views
ADD COMMENTlink modified 29 days ago by Juke344.9k • written 29 days ago by karthic100
0
gravatar for Juke34
29 days ago by
Juke344.9k
Sweden
Juke344.9k wrote:

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

ADD COMMENTlink written 29 days ago by Juke344.9k

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
ADD REPLYlink modified 28 days ago • written 28 days ago by karthic100
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