About Cuffcompare output

Question

[R.Blues]

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.

[Benn]

Did you read the manual?

http://cole-trapnell-lab.github.io/cufflinks/cuffcompare/index.html