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Old 05-11-2016, 01:21 AM   #5
Jane M
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Location: Paris

Join Date: Aug 2011
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Thank you dpryan for your answer.

Quote:
Originally Posted by dpryan View Post
UCSC references...kind of suck.
Don't you thing this refFlat reference is sufficient for experiments with polyA RNA selection?


Quote:
Originally Posted by dpryan View Post
Use Gencode/Ensembl and you'll get more complete coding and non-coding transcripts. Having said that, for lincRNAs you might want to check out lincrnadb or RNAcentral.
Since I am working with hg19 annotation, I downloaded the gtf from http://www.gencodegenes.org/releases/19.html for "ALL" regions, that is the gencode.v19.chr_patch_hapl_scaff.annotation file. I am not familiar with these annotation files. Is it the right one?

I am currently looking at what this file contains: number of genes (name, ID, status), transcripts, ...
It has not the same format like the refFlat file, so I expect some issues for read counting.
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