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Old 09-14-2012, 09:19 AM   #1
golharam
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Default GTF file from UCSC with Gene name???

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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Old 09-14-2012, 02:11 PM   #2
dariober
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Quote:
Originally Posted by golharam View Post
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???
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.

A sample output for the Actb gene in mouse looks like this:
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";
The iGenomes also have GTF files http://cufflinks.cbcb.umd.edu/igenomes.html.

Hope this helps!

Dario
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Old 09-17-2012, 12:28 PM   #3
golharam
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yes, thank you!
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