Does the order of trimming reads first and then filterings or first filtering reads and then trimming make a diffrence?
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seraphya •
Ideally both should give same results. If you are trimming first, you should reduce the cutoff for read quality while filtering the reads.
By reducing the cutoff do you mean keeping more reads or discarding more reads?
If I get your question right you mean trimming of ends and filtering based on quality values, taking that the mean quality is not too bad.
I would suggest you to remove the highly ambiguous reads based on the N's% (>=50)in them, then go for error correction with tools such as Musket (the only one I have used). http://musket.sourceforge.net/homepage.htm#latest
Keep in mind that the quality values do not change after musket, so the quality filter is nor more necessary.
So, Remove ambiguity and then Error-correction.
After doing all this, you will not have to worry about trimming your ends or quality filter again.
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Do you mean, "Does the order of adaptor and base quality trimming matter?" Otherwise, which sort of trimming and filtering do you have in mind?
I mean filtering reads out by quality