Question: Sliding window in Trimmomatic and PrinSeq
0
gravatar for seta
23 months ago by
seta1.1k
Sweden
seta1.1k wrote:

Hi all,

I read "Trimmomatic slides the window from the beginning (5′ end) of the read, whereas PrinSeq allows one to decide from which end the scanning should start. Note that sliding the window from the 5′ end keeps the beginning of the read until the quality falls below the threshold while sliding from the 3′ end cuts until it reaches a window with good enough quality", in a book. I'm confused with "while sliding from the 3′ end cuts until it reaches a window with good enough quality" sentence.

Could you please explain to me how sliding window work in PrinSeq?

Thanks

trimming sliding window • 818 views
ADD COMMENTlink modified 23 months ago • written 23 months ago by seta1.1k

Window-based trimming is not optimal... it's best to use the Phred algorithm, which produces optimal results (assuming the q-scores are accurate).

ADD REPLYlink written 23 months ago by Brian Bushnell16k
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