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jpuritz / dDocent

a bash pipeline for RAD sequencing
ddocent.com
MIT License
53 stars 41 forks source link

early organization #44

Closed pdimens closed 4 years ago

pdimens commented 5 years ago

includes code cleanup and distinct folder structure

but .fq.gz cant find files in the main folder.

pdimens commented 5 years ago

So the value is the window size? I'm a little confused :/

jpuritz commented 5 years ago

I believe that --cut-front or --cut-tail activates the sliding window trimming, and --cut_mean_quality and --cut_window_size set parameters of the sliding window. There are default values to the later two, so --cut-front or --cut-tail will work without other parameters set.

pdimens commented 5 years ago

Ah, OK. That's what I initially thought. Thanks.

Pavel