I have mapped paired end reads to my reference genome using TopHat and then obtained FPKM values through Cufflinks. I ran cufflinks without a gtf file as I am doubtful about its quality.
I was wondering how transcripts and exons were assigned in the transcripts.gtf output? Without a gtf file how are exons grouped together into transcripts? (see below)
Additionally, these transcripts are present in the genes.fpkm_tracking file but without length or coverage information. What does this mean about these transcripts?
gi|321228270|ref|NW_003456354.1| Cufflinks transcript 47231 73196 808 - . gene_id "CUFF.7"; transcript_id "CUFF.7.1"; FPKM "10.0383916498"; frac "0.494670"; conf_lo "9.300440"; conf_hi "10.776343"; cov "33.488707";
gi|321228270|ref|NW_003456354.1| Cufflinks exon 47231 48414 808 - . gene_id "CUFF.7"; transcript_id "CUFF.7.1"; exon_number "1"; FPKM "10.0383916498"; frac "0.494670"; conf_lo "9.300440"; conf_hi "10.776343"; cov "33.488707";
gi|321228270|ref|NW_003456354.1| Cufflinks exon 48894 49044 808 - . gene_id "CUFF.7"; transcript_id "CUFF.7.1"; exon_number "2"; FPKM "10.0383916498"; frac "0.494670"; conf_lo "9.300440"; conf_hi "10.776343"; cov "33.488707";
gi|321228270|ref|NW_003456354.1| Cufflinks exon 49688 49882 808 - . gene_id "CUFF.7"; transcript_id "CUFF.7.1"; exon_number "3"; FPKM "10.0383916498"; frac "0.494670"; conf_lo "9.300440"; conf_hi "10.776343"; cov "33.488707";
gi|321228270|ref|NW_003456354.1| Cufflinks exon 50723 50852 808 - . gene_id "CUFF.7"; transcript_id "CUFF.7.1"; exon_number "4"; FPKM "10.0383916498"; frac "0.494670"; conf_lo "9.300440"; conf_hi "10.776343"; cov "33.488707";
Any help would be much appreciated,
Thanks