Feature Request: Ensembl ID alongside gene name in expression table

[duyck]

There are over 100 ensembl genes with the same name. Would be helpful to have unique identifiers used alongside gene names.

[Hoohm]

The gene name selection is done in the Drop-seq tools which are written in java and not available.
One hack would be to just copy the gene ID in the gene name filed in the gtf file. But this is kind of messy.

[Hoohm]

@duyck
I found out there is an option to get multiple genes on top of the read in the TagReadWIthGeneExon.
ALLOW_MULTI_GENE_READS=BooleanAllow
The only problem is that it would use a comma separated gene name, which is probably not satisfactory.

I can still expose the option if you want.

[colindaven]

Identifiers would be great. These are necessary for pathway analysis, eg. in the R/Shiny Single Cell Toolkit.