Hello everyone, I am student in bioinformatics but I am not a statician...

I'm working with cufflinks package to run my experiments and I'm doing well with that. But I am developing a web tool to better show my work to my work group and make their job easier too.

I was wondering if can I change the cuffdiff output to calculate the average read count across all samples of my experiment, as LogCPM and Base Mean of the edgeR and DESeq2 respectively.

Looking in genes.count_tracking I found gene counts for each condition, but how can I convert and normalize then to what I am looking for? As I said, I am not a statistician and I don't know what I do.

Any news will be welcome. Thanks for your time :)