Hi,
I am doing a de novo comparative transcriptome analysis to compare two samples.
I first generated a transcriptome based on Velvet/Oases assembly for both samples merged, and the output, as I understand it, is a set of isotigs.
I then aligned the reads from each sample to the assembled transcriptome to find expression using Tophat and compared both samples using Cufflinks.
My question is that, apart from comparing each entry in the reference generating the gene_exp.diff file (in this case isotigs), which I think is ok, Cufflinks (cuffdiff) also detects alternative splicing (isoform_exp.diff file) but from a reference that is supposedly formed by isoforms, but this result is not relevant in this case.
Is my reasoning correct?
Any help will be greatly appreciated
D.
I am doing a de novo comparative transcriptome analysis to compare two samples.
I first generated a transcriptome based on Velvet/Oases assembly for both samples merged, and the output, as I understand it, is a set of isotigs.
I then aligned the reads from each sample to the assembled transcriptome to find expression using Tophat and compared both samples using Cufflinks.
My question is that, apart from comparing each entry in the reference generating the gene_exp.diff file (in this case isotigs), which I think is ok, Cufflinks (cuffdiff) also detects alternative splicing (isoform_exp.diff file) but from a reference that is supposedly formed by isoforms, but this result is not relevant in this case.
Is my reasoning correct?
Any help will be greatly appreciated
D.