GTF file with one line per gene?

[cnyh]

I would like to use bedtools to extract raw gene counts from my .bam files. However, I was using UCSC_Genes.gtf (human) as my source file, but that file contains multiple lines for each gene, which is an issue since the output from bedtools is in the same format.

Where can I find a .gtf file containing only a single line for each gene? Preferably with Entrez gene IDs if this is easily available.

[iris_aurelia]

Why don't you give HTSeq-count a try? It takes a GTF file and a sam file as an input and outputs counts per gene for each gene in the GTF file.

[cnyh]

That does look very helpful indeed. Thanks for the tip!

[crazyhottommy]

check here:http://genomewiki.ucsc.edu/index.php..._or_gff_format