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Old 06-28-2016, 01:37 AM   #128
fkrueger
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Location: Cambridge, UK

Join Date: Sep 2009
Posts: 614
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Hi Guorong,

Great that it is working. My thoughts to your other problem are, as I have outlined above already, that you should absolutely not be doing what you are suggesting here. The sequence you are after is the sequence from the start of the read until you hit the small RNA adapter which starts with TGGAATTCT... Everything after that is either adapter that binds to the flowcell or something else you don't want to keep. In any case, the sequence on the 3' end should not align to a genome anyway.

Code:
  -g ADAPTER, --front=ADAPTER
                        Sequence of an adapter that was ligated to the 5' end.
Illumina sequencing does not add any adapter to the 5' end that ends up being sequenced, hence trimming using the option -a is what you want to do. In my opinion if you just run
Code:
 trim_galore --trim-n file
you would get exactly what you are looking for.
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