Closed DarioS closed 7 years ago
This is caused by a bug in the GENCODE genes lift-over software and will be fixed by GENCODE version 26, according to the GENCODE project support staff. Therefore, rsem-prepare-reference
doesn't need to accommodate this.
Hi @DarioS , glad to hear that the issue is resolved.
GENCODE Genes sometimes uses the same gene symbol twice or more. For example,
The transcripts associated with these duplicated gene symbols have identically located exons, introns, and UTRs. I notice that even if I see reads mapped to the genome overlapping these kinds of genes, RSEM will calculate an expected count of 0 for both genes in all samples in
genes.results
. Shouldn'trsem-prepare-reference
handle this case better?