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Old 01-16-2019, 11:11 PM   #134
badhik
Junior Member
 
Location: New England

Join Date: Jan 2019
Posts: 2
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Hi all,

I am trimming Illumina 1.9 encoded data with Trim-galore, and after Fastqc, the box-plot whiskers under the Per base sequence quality goes all the way to 13 or 14 Phred score.

Here is what I used:
trim_galore --rrbs --paired --length 20 -q 28 --illumina

Why am I getting such a result?

Thanks
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