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Old 09-03-2015, 08:48 AM   #1
Location: Munich

Join Date: Jul 2015
Posts: 14
Default Cufflinks and hg38 annotation

Dear all,

I would like to run cufflinks with reads aligned to the human GRCh38/hg38 genome assembly (download from UCSC). Cufflinks requires an annotation file with tss_id and p_id to allow differential expression analysis. I did not yet find any source of such gtf file. Is there anyone out there who could offer such file or know a location for download? Or am I stuck with hg19?


BTW: I did run liftOver from the Illumina hg19 GTF, but liftOver warns me that this is not reliable. So before spending a lot of time on this file, I'd like to hear your suggestions.

Last edited by abisko00; 09-03-2015 at 08:52 AM.
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