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Hi,
I ran cufflinks 2.0.2 on our data (7 samples in total) and then used cuffmerge to merge transcripts. However, I found cuffmerge reports transcripts that are not included in transcripts.gtf of any sample or in the provided reference gtf. Has anyone have similar experience with this? I also got the same results from cufflinks 1.3.0.
I attached a figure here. The middle track is merged.gtf, with four transcripts. The last transcript in this track is not seen in any sample.
This affects the downstream cuffdiff analysis, since the addition of the new transcript might make it impossible to determine to which transcript some exons belong.
Am I missing something? I will appreciate if anyone can shed some lights into this.
Thanks!
I ran cufflinks 2.0.2 on our data (7 samples in total) and then used cuffmerge to merge transcripts. However, I found cuffmerge reports transcripts that are not included in transcripts.gtf of any sample or in the provided reference gtf. Has anyone have similar experience with this? I also got the same results from cufflinks 1.3.0.
I attached a figure here. The middle track is merged.gtf, with four transcripts. The last transcript in this track is not seen in any sample.
This affects the downstream cuffdiff analysis, since the addition of the new transcript might make it impossible to determine to which transcript some exons belong.
Am I missing something? I will appreciate if anyone can shed some lights into this.
Thanks!