When I did RNA-Seq analysis, the GTF file I used was from Ensembl. The output of cuffdiff replaced the Ensembl IDs with XLOC's although it also output gene names (e.g. MX2). Ensembl IDs were no longer there.
Is there anyway to convert XLOC back to Ensemble IDs, or simply keep the ensembl IDs from my GTF file? how do you guys go about this?
Interesting enough, if I don't run new gene discovery (i.e. without doing cuffmerge step), I got to keep Ensembl IDs.
Is there anyway to convert XLOC back to Ensemble IDs, or simply keep the ensembl IDs from my GTF file? how do you guys go about this?
Interesting enough, if I don't run new gene discovery (i.e. without doing cuffmerge step), I got to keep Ensembl IDs.
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