chapmanb/bcbio-nextgen — pull request #263 by mjafin (2014-01-20 15:30:22+00:00)
Title: Added option of reporting gene_name instead of gene_id in htseq count files

Hi Brad and Rory,
Would you be willing to expose one more setting for RNA-seq, namely reporting of gene_name instead of gene_id in the htseq-count files? Most biologists want to see the gene names and are allergic to Ensembl IDs..

Happy to rename any parameters in any way you see fit. (Further work would be needed to extend this to Cufflinks but it might be tricky as the transcript names are not in the gtf) Also happy to mention this in the documentation if you're willing to accept the pull request.