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Old 03-28-2018, 09:27 AM   #6
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Location: East Coast USA

Join Date: Feb 2008
Posts: 6,800

Best solution is to get the sequence/annotation bundle from Illumina's iGenomes site (note: link is for big file download). In that download you will find a genes.gtf file in Annotation/Genes folder. Use that for your counting.

I also recommend that you use featureCounts. Much faster and easier to use.
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