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Old 05-10-2013, 01:38 AM   #2
Jeremy
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Location: Pathum Thani, Thailand

Join Date: Nov 2009
Posts: 190
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TRIMMOMATIC, or any other read cleaning program, should clean those up. I would use options: SLIDINGWINDOW:4:15 HEADCROP:15 MINLEN:36
Then run FastQC again and you should see a much nicer report, if you are just mapping to a reference genome then cleaning reads is less of an issue so you could leave out the HEADCROP (which cuts bases from the start). But if you are assembling de-novo then I would cut that non-random sequence at the start.
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