SEQanswers - View Single Post - Which feature file for htseq-count for non coding elements of ribodepleted samples?

GenoMax · 05-12-2016, 06:43 AM

Why are you not using the GTF file from UCSC instead of all those other files. You could create that from Table Browser. (iGenomes bundle does not have non-coding genes).

Edit: @Vikas Bansal has a solution to get the non-coding elements (you can choose GTF output in table browser) for hg19 here.

05-12-2016, 06:43 AM	#11
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,091	Why are you not using the GTF file from UCSC instead of all those other files. You could create that from Table Browser. (iGenomes bundle does not have non-coding genes). Edit: @Vikas Bansal has a solution to get the non-coding elements (you can choose GTF output in table browser) for hg19 here. Last edited by GenoMax; 05-12-2016 at 06:54 AM.