Fixing Up Read Quality: Trimming First Or Filtering First?

Question

[seraphya]

Does the order of trimming reads first and then filterings or first filtering reads and then trimming make a diffrence?

[Devon Ryan]

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?

[seraphya]

I mean filtering reads out by quality

Answer 1

[GouthamAtla]

Ideally both should give same results. If you are trimming first, you should reduce the cutoff for read quality while filtering the reads.

[seraphya]

By reducing the cutoff do you mean keeping more reads or discarding more reads?

Answer 2

[Rohit]

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.