i want to compare the ontologies of genes generated from cuffdiff output and use it for BLAST2GO. Tried several options but for BLAST2GO , a fasta seq is required so i used gffread and then extract genomic DNA for fasta sequence . i have used the merged transcript file generated from cuffmerge . I dont know whether i am following the right track:
1. my aim is to compare the ontologies of differentially expressed genes in 2 samples
2. is there any way to know that which transcripts came from which sample because when i am using the merged transcript file it will give me the fasta seq but will it tell me which seq / transcript from which sample so that i can compare their ontologies in terms of gene expression.