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Old 02-11-2017, 05:04 AM   #4
mastal
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Location: uk

Join Date: Mar 2009
Posts: 667
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Are you sure you haven't made some kind of syntax error when running Bowtie after the trimming, or maybe there is something wrong with the format of the files after trimming?

Because, as you mentioned, cutadapt only removed adapters from a small number of reads, so you would expect at most a small difference in the number of reads aligned, and usually you would expect an improvement.
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