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

Join Date: Aug 2011
Posts: 239

Thank you dpryan for your answer.

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?

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 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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