I have supplied Tophat/Bowtie with a gtf file from Ensembl. However, instead of making use of the gene symbols (the column "gene_name" in the gtf file, for example "DDX11L1"), it seems to use the Ensembl gene ID's instead (the column "gene_id" in the gtf file, for example "ENSG00000223972").
How do I get Tophat/Bowtie to use the "gene_name" column instead? Is this possible?
How do I get Tophat/Bowtie to use the "gene_name" column instead? Is this possible?
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