Gene name is incorrectly replaced by biotype for GTF of which the gene_name field is missing

[shenyang1981]

Hello,

I was trying to run STARSolo on poorly annotated species Macaca fascicularis. The GTF file was downloaded from Ensembl (v95). For genes that don't have gene name annotated, the biotype was used by STARSolo to represent the gene name.

For example, gene "ENSMFAG00000010714" only gets gene_id annotated in GTF file.

(from GTF:)

1 ensembl gene 1174457 1175395 . - . gene_id "ENSMFAG00000010714"; gene_version "1"; gene_source "ensembl"; gene_biotype "protein_coding";

In the genes.tsv file generated by STARSolo, this gene was shown as:

ENSMFAG00000010714 protein_coding

And "protein_coding" was used as gene name (or row name) in count matrix (from matrix.mtx).

Please help fix this issue for those poorly annotation species. And it would be nice to offer an option to select gene_id/gene_name as the row name in count matrix. Thanks a lot.

Best,
Yang

[alexdobin]

Hi Yang,

thanks for reporting this problem, 2.7.1a should fix it.

Cheers
Alex