Hello,
I ’d like to test differential expression between two conditions (i.e. treatment vs control, without replicates) but taken into account isoforms. So, if I want to use DESeq, my question is how to obtain the raw counts from cufflinks and at the same time deal with the uncertainty in the assignment of reads to transcripts.
Thanks,
I ’d like to test differential expression between two conditions (i.e. treatment vs control, without replicates) but taken into account isoforms. So, if I want to use DESeq, my question is how to obtain the raw counts from cufflinks and at the same time deal with the uncertainty in the assignment of reads to transcripts.
Thanks,