Hi there,
Could anyone please help me to understand the difference between two output files of cuffmerge, merged.gtf (which is supposed to be final output) and trasncript.gtf.
I used cufflink to reconstruct a gene model from 3 time points and finally merged them using cuffmerge (with reference annotation). Two output files of cuffmerge are trasncript.gtf and merged.gtf. among others. Isn't the trasncript.gtf and merged.gtf suppose to be similar, or why aren't they similar?
I converted both .gtf files into .bed, and overlapped them, i found around 2000 transcripts from transcript.gtf were missing in merged.gtf ? Then i looked into those missing cases (in merged.gtf), those trasncripts have nice coverage and gene model is also present in individual time point.
So, why do we see this difference ?
Thank you for your help in advance !!
regards
Chirag
Could anyone please help me to understand the difference between two output files of cuffmerge, merged.gtf (which is supposed to be final output) and trasncript.gtf.
I used cufflink to reconstruct a gene model from 3 time points and finally merged them using cuffmerge (with reference annotation). Two output files of cuffmerge are trasncript.gtf and merged.gtf. among others. Isn't the trasncript.gtf and merged.gtf suppose to be similar, or why aren't they similar?
I converted both .gtf files into .bed, and overlapped them, i found around 2000 transcripts from transcript.gtf were missing in merged.gtf ? Then i looked into those missing cases (in merged.gtf), those trasncripts have nice coverage and gene model is also present in individual time point.
So, why do we see this difference ?
Thank you for your help in advance !!
regards
Chirag
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