I'm wondering what the results of cufflinks mean.
This is how they explaned:
In the transcripts.gtf, each row represents either a transcript or an exon within a transcript.
The isoforms.fpkm_tracking contains the estimated isoform-level expression values in generic FPKM.
The genes.fpkm_tracking contains the estimated gene-level expression values in the generic FPKM
I noticed two interesting things. (1) in the transcripts.gtf, there is a FPKM value which is from the isoforms.fpkm file and (2) All the entries from isoform.fpkm exist in transcripts.gtf. But exons may exist in several transcripts.
I don't know how the cufflinks exactly work but i guess, it assemble out all the possible transcripts in isoform tracking and exons in gene tracking, and list their composition relations in the transcripts.gtf file.
This is what I understand about cufflinks results, I warmly welcome any comments and discussions.
fangquan
This is how they explaned:
In the transcripts.gtf, each row represents either a transcript or an exon within a transcript.
The isoforms.fpkm_tracking contains the estimated isoform-level expression values in generic FPKM.
The genes.fpkm_tracking contains the estimated gene-level expression values in the generic FPKM
I noticed two interesting things. (1) in the transcripts.gtf, there is a FPKM value which is from the isoforms.fpkm file and (2) All the entries from isoform.fpkm exist in transcripts.gtf. But exons may exist in several transcripts.
I don't know how the cufflinks exactly work but i guess, it assemble out all the possible transcripts in isoform tracking and exons in gene tracking, and list their composition relations in the transcripts.gtf file.
This is what I understand about cufflinks results, I warmly welcome any comments and discussions.
fangquan