I am using package org.Mm.eg.db (org.Mm.egENSEMBL) to annotate the differential expressed genes (tophat(mm9)-featureCounts-RUVseq-edgeR). Although the results are nice some genes could not well being annotated and I guess it is is because I am using a GTF (NCBI37 mouse annotation) a bit different from that one used by org.Mm.egENSEMBL (both NCBI and ENSEMBL). Do you have suggestions of which GTF should I better use?
I am really interested in isoform transcript analysis, any tool suggestion? We have a batch effect, so I might be forced to use RUVseq tool or something similar before the analysis. I have tried cuffdiff but... not successful results to be honest.
Thanks a lot for your help!