Hello everyone,
I have run Cuffcompare between a reference GTF and a predicted GTF I obtained with the Cufflinks pipeline.
However, I am not sure I understand the output. I would appreciate if someone could explain it to me.
Specifically, the TCONS from my predicted GTF appear at the first column or at the sixth? I understand that they appear at the sixth, and that it is simply that Cuffcompare follows the same nomenclature as Cufflinks/Cuffmerge when denominating transfrags, but I would like someone to confirm it. I attach some results as an example
TCONS_00000019 XLOC_000009 GeneY|rna2 j q1:GeneY|TCONS_00000020|0|0.000000|0.000000|0.000000|0.000000|-
TCONS_00000020 XLOC_000010 GeneX|rna3 j q1:GeneX|TCONS_00000022|0|0.000000|0.000000|0.000000|0.000000|-
TCONS_00000021 XLOC_000010 GeneX|rna3 j q1:GeneX|TCONS_00000023|0|0.000000|0.000000|0.000000|0.000000|-
TCONS_00000022 XLOC_000010 GeneX|rna3 = q1:GeneX|TCONS_00000024|0|0.000000|0.000000|0.000000|0.000000|-
Also, biologically, what does it mean when there are two transcript IDs (sixth column) for the same transfrag ID (first column)? I guess that they are part of the same transfrag, but... Is that all?
Thank you very much for your help and time.
Did you read the manual?
http://cole-trapnell-lab.github.io/cufflinks/cuffcompare/index.html