[Feature Request] Quality trim both ends of a read

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The -q, --quality-trim option only applies to the 3' end. It would be helpful 
to have some way of trimming the 5' end as well, as there can be biases in 
RNA-Seq data on that end (http://nar.oxfordjournals.org/content/38/12/e131).

Original issue reported on code.google.com by ja...@broadinstitute.org on 4 Mar 2015 at 5:16

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Do you have an idea whether the algorithm that cutadapt currently uses for the 
3' end would also be appropriate for the 5' end?

Original comment by marcel.m...@tu-dortmund.de on 4 Mar 2015 at 9:29

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[deleted comment]

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I don't see why not

Original comment by ja...@broadinstitute.org on 4 Mar 2015 at 9:54

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I've just implemented this. Use something like "-q 10,15" to trim both ends: 
cutoff 10 is used for the 5' end, cutoff 15 is used for the 3' end. As before, 
if you use "-q 15", only the 3' end is trimmed. The change will be in cutadapt 
1.8, which I’m planning to release within the next days.

Original comment by marcel.m...@tu-dortmund.de on 13 Mar 2015 at 10:49

• Changed state: Fixed
• Added labels: Type-Enhancement
• Removed labels: Type-Defect

[GoogleCodeExporter]

Awesome, thanks! 

Original comment by ja...@broadinstitute.org on 13 Mar 2015 at 1:40