How can I group my transcript from gffcompare result?
Hello,
I am new to gffcompare/cuffcompare and now I am confused with the output file.
I have used SMRTAnalysis Iso-Seq pipline to get isoforms from pacbio sequencing data. Now I want to classify the isoforms into different groups by comparing with reference annotation(*.gff files). By using gffcompare, I get the classcode (eg. =,c,j,e,i,o,p,r,u,x,s) information for my isoform, how can I classify the novel isofroms from novel genes, novel transcript from known gene, known transcript by classcode? And how can I identify novel loci from the output file gffcompare.loci?
Thanks a lot for any reply!
I am new to gffcompare/cuffcompare and now I am confused with the output file.
I have used SMRTAnalysis Iso-Seq pipline to get isoforms from pacbio sequencing data. Now I want to classify the isoforms into different groups by comparing with reference annotation(*.gff files). By using gffcompare, I get the classcode (eg. =,c,j,e,i,o,p,r,u,x,s) information for my isoform, how can I classify the novel isofroms from novel genes, novel transcript from known gene, known transcript by classcode? And how can I identify novel loci from the output file gffcompare.loci?
Thanks a lot for any reply!
