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alexstaj / cutadapt

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just trim quality #22

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
Would cutadapt doesn't trim adapter but just quality? May i just use -q option 
independently?

felix

Original issue reported on code.google.com by funal.zh...@gmail.com on 7 Jun 2011 at 2:17

GoogleCodeExporter commented 9 years ago 
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.

Original comment by marcel.m...@tu-dortmund.de on 7 Jun 2011 at 7:59

GoogleCodeExporter commented 9 years ago

Original comment by marcel.m...@tu-dortmund.de on 7 Jun 2011 at 7:59

GoogleCodeExporter commented 9 years ago 
May i ask a question?

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

felix

Original comment by funal.zh...@gmail.com on 7 Jun 2011 at 9:59

GoogleCodeExporter commented 9 years ago 
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."

Original comment by marcel.m...@tu-dortmund.de on 7 Jun 2011 at 1:39

GoogleCodeExporter commented 9 years ago 
You explained it in detail. Thanks a lot.
cutadapt is a very useful, powerful and simple to use.

felix

Original comment by funal.zh...@gmail.com on 7 Jun 2011 at 6:01

GoogleCodeExporter commented 9 years ago 
I'm happy to help, thanks for using cutadapt.

Original comment by marcel.m...@tu-dortmund.de on 8 Jun 2011 at 8:15

GoogleCodeExporter commented 9 years ago 
This feature has now been implemented and will be in cutadapt version 1.1.

Original comment by marcel.m...@tu-dortmund.de on 12 May 2012 at 9:09