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

Join Date: Feb 2010
Posts: 994
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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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