I am new to bioinformatics and please help me with this.
I used Star-Cuffdiff pipeline without cufflink to get DEG analysis. When I run cuffdiff with default settings, I got gene expression data. When we try to validate highly expressed genes by qPCR, those genes are undetectable.
So, my question is, where could be the problem? What can I do in this case? My library is truqseq fr firsstarnd ,
So I run cuffdiff again with library type , c flag, and b flag and then I keep receiving an error message saying labels should match the number of conditions. So, I retired again with the same code removing these advanced options, then it works fine.
I have spent a lot of time on searching for this error, but could not get any useful information.
Please help me out. Thanks for taking the time to read.
Sincerely , Aynur