For my analysis using DEXSEQ, firstly I used following command to generate a GFF file:
dexseq_prepare_annotation.py ../Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf Mus_musculus.NCBIM37.DEXSeq.chr.gff
then i obtained a count file by running
this returned a text output as:
My question is,
Is there a way I could map these exon files (ENMUSG:001) to their corresponding transcript ID (ENSMUST)?
Is it possible to get the output in form of ENSMUSE* instead of ENMUSG:001 etc. Then I can use biomart to map them.