Here's a simple question...I have a list of gene names that I want to retrieve a GTF file of those genes specifically. I put the list into UCSC for RefSeq genes and download the GTF file. The resulting GTF files does NOT contain the gene names, only the gene id's. So, how do I get a GTF file with the gene names???
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Maybe what you want is the refFlat table from UCSC? Select Group: Gene and Gene prediction tracks; Track: RefSeq genes; Table: refFlat. Output format: GTF.Originally posted by golharam View Post
A sample output for the Actb gene in mouse looks like this:
The iGenomes also have GTF files http://cufflinks.cbcb.umd.edu/igenomes.html.Code:chr5 mm10_refFlat stop_codon 142903798 142903800 0.000000 - . gene_id "Actb"; transcript_id "Actb"; chr5 mm10_refFlat CDS 142903801 142903941 0.000000 - 0 gene_id "Actb"; transcript_id "Actb"; chr5 mm10_refFlat exon 142903116 142903941 0.000000 - . gene_id "Actb"; transcript_id "Actb"; chr5 mm10_refFlat CDS 142904067 142904248 0.000000 - 2 gene_id "Actb"; transcript_id "Actb"; chr5 mm10_refFlat exon 142904067 142904248 0.000000 - . gene_id "Actb"; transcript_id "Actb"; chr5 mm10_refFlat CDS 142904344 142904782 0.000000 - 0 gene_id "Actb"; transcript_id "Actb"; chr5 mm10_refFlat exon 142904344 142904782 0.000000 - . gene_id "Actb"; transcript_id "Actb"; chr5 mm10_refFlat CDS 142905237 142905476 0.000000 - 0 gene_id "Actb"; transcript_id "Actb"; chr5 mm10_refFlat exon 142905237 142905476 0.000000 - . gene_id "Actb"; transcript_id "Actb"; chr5 mm10_refFlat CDS 142905564 142905686 0.000000 - 0 gene_id "Actb"; transcript_id "Actb"; chr5 mm10_refFlat start_codon 142905684 142905686 0.000000 - . gene_id "Actb"; transcript_id "Actb"; chr5 mm10_refFlat exon 142905564 142905692 0.000000 - . gene_id "Actb"; transcript_id "Actb"; chr5 mm10_refFlat exon 142906652 142906724 0.000000 - . gene_id "Actb"; transcript_id "Actb";
Hope this helps!
Dario -
yes, thank you!Comment
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