Hi. I started a RNAseq analysis last week and I’m on the final steps, but I’m unable to get cummeRbund to make expression plots. I ran cuffdiff normally with a gtf file (hg38 refseq annotation) and got the sq lite database. It does generate density plots and heatmeaps correctly, of which the latter ones require gene ids. It takes some seconds to trace the gene ids and it appears as “no option available” for some seconds but it eventually lets me choose. This doesn’t happen for expression plots since it doesn’t trace the gene ids for some reason and I don’t know how to fix it. I’ve tried to annotate my IDS but it didn’t help. What seems to be the problem?
I have not used Cuffdiff for ages and cannot help much, but maybe try GenCode gene annotation. I found their annotations very reliable.
You may also consider DGE analysis using featureCount and limma-voom/edgeR/DESeq2: