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Old 05-12-2016, 07:26 AM   #12
Jane M
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Location: Paris

Join Date: Aug 2011
Posts: 239

Originally Posted by GenoMax View Post
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).
I was actually using only the refFlat gtf from UCSC. It looks like what I showed.
I added the refGene and knownGenes gtf files to show that these files do not contain description neither.
There seem to be some non coding elements in refFlat gtf: ~900 LINC, ...

Originally Posted by GenoMax View Post
Edit: @Vikas Bansal has a solution to get the non-coding elements (you can choose GTF output in table browser) for hg19 here.
Thank you, I will take a look. But it is probably easier to use genecode to get everything from a single gtf file.
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