Entering edit mode
8.1 years ago
dina.hesham139
▴
170
Hey,
I have an issue of not getting any expression values for CDS following: HISAT2 (against hg19) --> cufflinks--> cuffmerge/or cuffcompare--> cuffdiff. Knowing that I do use an annotation file that has the p_ids in the relevant steps.
On the other hand, when I go directly from HISAT2 --> cuffdiff (using the original annotation file and not the merged one of all the assemblies), only then I got expression values for CDS.
I know that the second approach won't give me the novel transcripts/isoforms. So, is it a sound approach? If I want to stick to the first approach? what would I do to get the CDS values?
Thank you!
