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Old 02-25-2014, 10:39 PM   #4
Simon Anders
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Location: Heidelberg, Germany

Join Date: Feb 2010
Posts: 994
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Have you had a look at the alignments yet? Pick a two or three genes for which the counts between stranded and unstranded libraries differ strongly and two or three genes for which they agree reasonably well, then look at the eads at these loci with a genome browser (e.g., IGV). Do you see antisense transcripts which should not be there? Do you see many reads with low alignment quality? Any other peculiarity?
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