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Old 08-26-2016, 07:50 AM   #1
Location: New haven

Join Date: May 2013
Posts: 47
Default Deprecated gene IDs, HELP!!!

Dear All,

I have done some RNAseq analysis of mice tissues - regular mRNA enrichment, 2X75 PE, 30M reads per sample.

I aligned with tophat2 (GRCm38) and used HTSeq for raw gene count.
Normalization and statistics done with edgeR.

All the stats look good and the differential gene expression makes sense.
However, in my list of genes I have a lot (a LOT!) of transcripts that are deprecated in the current assembly of Ensembl.
As a result I have a lot of genes with an Ensembl ID and without an associated gene name.
Even trying Biomart I am not able to translate those IDs into something meaningful.

Does anyone have suggestions?!?!?

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