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Old 03-22-2013, 10:55 AM   #4
Simon Anders
Senior Member
Location: Heidelberg, Germany

Join Date: Feb 2010
Posts: 994

The newest version now doesn't show these warnings any more, so maybe try again with that one.

Also, in general, if you want to catch the error messages printed by a shell command into a file, use the '2>' operator:

htseq-count -s reverse -q 21allsort.sam ./../igenome.mm10.mouse.genes.gtf > 21all.counts 2> error.log
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