A Feature to use gene ID instead of gene names

[WellSIM]

My scope: I want to implement Dropseq for total RNA seq.

Function:

1. TagReadWithGeneFunction
   Issue: the gene ID without gene names and transcript were removed. Mostly, those are from miRNA.
   Request: a feature that retain gene ID whose without gene name and/or transcript.

2. Digital Gene Expression
   Issue: Only return gene names
   Request: a feature return gene names, gene ID, and gene biotype.

[jamesnemesh]

Without changing dropseq software, here are some potential workarounds:

1. Modify your GTF so that gene names are replaced by gene IDs where appropriate. You might perform this for all records to be consistent.
2. There's no place to store these metadata fields in the existing DGE format, but that doesn't prevent you from generating them from your GTF file directly. If you change your gene names in step 1, then the output files will reflect those IDs and you should be able to perform a lookup.