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Old 01-15-2014, 11:22 AM   #5
mastal
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Location: uk

Join Date: Mar 2009
Posts: 667
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@clintp

I think the parameters you are using for the IlluminaClip step (2:30:10 ) are too high for trimmomatic to recognize a match to a 13-base adapter sequence;

You need to either change the values or use a longer adapter sequence.

See the trimmomatic web page,

http://www.usadellab.org/cms/?page=trimmomatic

particularly the discussion under the heading 'Adapter Fasta', from which I have extracted this quote:

'The thresholds used are a simplified log-likelihood approach. Each matching base adds just over 0.6, while each mismatch reduces the alignment score by Q/10. Therefore, a perfect match of a 12 base sequence will score just over 7"
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