just trim quality

[marcelm]

From funal.zh...@gmail.com on June 07, 2011 04:17:33

Would cutadapt doesn't trim adapter but just quality? May i just use -q option independently?

felix

Original issue: http://code.google.com/p/cutadapt/issues/detail?id=22

[marcelm]

From marcel.m...@tu-dortmund.de on June 07, 2011 00:59:12

Because cutadapt requires that you specify at least one adapter, you cannot use the -q option independently. For now, you can just specify an adapter that doesn't occur anywhere, like "XXXXXXX". Until I've decided whether to remove the requirement that at least one adapter needs to be given, I'll leave this issue open.

[marcelm]

From marcel.m...@tu-dortmund.de on June 07, 2011 00:59:34

Labels: -Type-Defect Type-Enhancement

[marcelm]

From funal.zh...@gmail.com on June 07, 2011 02:59:38

May i ask a question?

How do i set up the -q cutoff value? Is it based on Phred score(0~40) ?

felix

[marcelm]

From marcel.m...@tu-dortmund.de on June 07, 2011 06:39:11

Yes. On FASTQ files, cutadapt assumes that quality values are encoded as ASCII(qual+33). See also this section from the README:

"The '-q' (or --trim-qualities) parameter can be used to trim low-quality ends
from reads before adapter removal. For this to work correctly, the quality
values must be encoded as ascii(phred quality + 33). If they are encoded as
ascii(phred quality + 64), you currently have to add 31 to the cutoff. For
example, if you actually mean "-q 10", you have to write "-q 41".

The trimming algorithm is the same as the one used by BWA. That is: Subtract
the given cutoff from all qualities; compute partial sums from all indices to
the end of the sequence; cut sequence at the index at which the sum is minimal."

[marcelm]

From funal.zh...@gmail.com on June 07, 2011 11:01:41

You explained it in detail. Thanks a lot.
cutadapt is a very useful, powerful and simple to use.

felix

[marcelm]

From marcel.m...@tu-dortmund.de on June 08, 2011 01:15:01

I'm happy to help, thanks for using cutadapt.

[marcelm]

From marcel.m...@tu-dortmund.de on May 12, 2012 14:09:58

This feature has now been implemented and will be in cutadapt version 1.1.

Status: Fixed