So, I've run tophat, cufflinks and cuffdiff from my rna seq.
Using the Broad institute provided gtf files, the programs mapped finely and I observed that some new transcripts were discovered. However, when I blast the resulting "new transcript" sequence to the reference genome, I got a perfect alignment to a know gene (already present in the GTF file). This is very weird. But the more confused thing is that the "new gene" shows differential expression, while the correct gene do not! For consider differntial expression, what should I do? sum the FPKM?
The transcripts were not identified as a result of differential splicing.
Any suggestions?
Thanks
Charley
Using the Broad institute provided gtf files, the programs mapped finely and I observed that some new transcripts were discovered. However, when I blast the resulting "new transcript" sequence to the reference genome, I got a perfect alignment to a know gene (already present in the GTF file). This is very weird. But the more confused thing is that the "new gene" shows differential expression, while the correct gene do not! For consider differntial expression, what should I do? sum the FPKM?
The transcripts were not identified as a result of differential splicing.
Any suggestions?
Thanks
Charley
