Hi,
When using the -G option in TopHat/Cufflinks, the manual states that the "Output will include all reference transcripts as well as any novel genes and isoforms that are assembled."
Where can I see these novel genes or the expression data for them? They don't seem to be reported...
Do I need to use another option or carry out further processing prior to using CuffDiff? I don't think I can use cuffmerge as it doesn't generate GTF files for each replicate when using the -G option.
Thanks
2 answers
you need to use cuffmerge. From manual of cuffmerge:
If you have a reference GTF file available, you can provide it to the script in order to gracefully merge novel isoforms and known isoforms and maximize overall assembly quality
My understanding is that cuffmerge generates master gtf file (master transcriptome) for further use in pipeline. If one includes reference gtf in cuffmerge step, Cuffdiff output will have details about the origin of transcripts (whether its from reference or novel).
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