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Old 05-11-2016, 02:46 AM   #7
Jane M
Senior Member
Location: Paris

Join Date: Aug 2011
Posts: 239

Originally Posted by dpryan View Post
The UCSC file annotations are never that good. The file you downloaded is fine, though again the chromosome names probably differ, which is what's causing problems. I think featureCounts can handle the chromosome naming difference internally, so try using that instead (it's much faster anyway).
Thank you again. No problem yet, since I did not try to count. Looking at the file: now, I have ~56600 different gene names, compared to ~26600 with refFlat. The file contains twice more lines. Looking forward to see how the number of LINC and AS will increase.
chr1->22, chrX, chrY have the same names, but the additional chromosomes have indeed different names: chr17_ctg5_hap1, chr17_gl000205_random in refFlat and GL000191.1, GL000192.1. I start the tests right now!
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