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I'm looking for an easy to use perl script for quality trim my Hi-seq reads (fastaq format).
Thanks
Thanks
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try..
SolexaQA package, which includes DynamicTrim... trims to the longest contiguous read segment above a quality cutoff that you set. Just google solexaqa..
There are lots of other ones out there.. you could also use the tools on Galaxy (google: galaxy penn state university) -
Thanks, I will try the SolexaQA package, Galaxy takes too long to download my data to the web site and to install Fastx in my computer is more complicated that what I thought!Comment
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worked well for me. Dynamictrim is just a perl script, easy to use, SolexaQA is a bit more complicated. I've done a bit of work that suggests that dynamictrim is a bit too stringent in it's default settings, but that depends on the quality of your run. but maybe try multiple trims at different stringencies and see how your assembly works out.Comment
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You can also have a look at ConDeTriComment
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