paired-end trimming - Githubissues

alexstaj / cutadapt

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paired-end trimming #14

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago

See
http://seqanswers.com/forums/showpost.php?p=38011&postcount=36

Original issue reported on code.google.com by marcel.m...@tu-dortmund.de on 26 Mar 2011 at 10:35

GoogleCodeExporter commented 9 years ago

Note: Since some versions of Bowtie cannot deal with empty reads, read pairs in 
which one of the reads is empty should possibly be removed entirely. (Perhaps 
optionally.)

Original comment by marcel.m...@tu-dortmund.de on 13 Jul 2011 at 1:42

GoogleCodeExporter commented 9 years ago

As I have received another request for this feature, I'll try to prioritize it.

Original comment by marcel.m...@tu-dortmund.de on 6 Oct 2011 at 12:41

Added labels: Priority-High
Removed labels: Priority-Medium

GoogleCodeExporter commented 9 years ago

I would like this too, but I think this issue is a little underspecified.  Are 
both pairs supposed to be trimmed?

My use case is to trim one file and to retain the corresponding set of reads in 
the second file that pass the read filter.  i.e. the discarded reads should 
have their pairs discarded too.

This handles this case, but trimming both pairs requires more surgery:
https://github.com/jamescasbon/cutadapt/compare/pe

Original comment by cas...@gmail.com on 7 Mar 2012 at 1:45

GoogleCodeExporter commented 9 years ago

Great, thanks for the patch! It’ll need a unit test and some documentation, 
however. I’ll be on holiday for two weeks, won’t be able to add this to 
cutadapt before that.

Original comment by marcel.m...@tu-dortmund.de on 9 Mar 2012 at 10:37

GoogleCodeExporter commented 9 years ago

Hi!

In principle both reads should be discarded because they are going to be too 
small, but sometimes cutadapt is able to remove one side but not the other 
because a lower quality sequencing.

What I have done as a transitory solution is to modify a little bit the program 
to output a read of Ns when the resulting read is too small and is going to be 
discarded. In this way the order of the pairs is kept between both files and it 
is left to the aligner what to do with a low quality read pair.

I guess the best solution would be to make cutadapt to deal with two paired 
files at the same time and remove the pair when one of the reads is too small.

Carlos

Original comment by ctorr...@googlemail.com on 31 May 2012 at 11:02

GoogleCodeExporter commented 9 years ago

This would be a great feature! Any progress?

Original comment by daniel.k...@gmail.com on 29 Jun 2012 at 7:45

GoogleCodeExporter commented 9 years ago

Rebased this on head: 
https://github.com/marcelm/cutadapt/pull/1

Original comment by cas...@gmail.com on 29 Jun 2012 at 2:08

GoogleCodeExporter commented 9 years ago

I think it is better to padding short or zero reads to a given length with 'N' 
and quality=2 .

Original comment by galaxy...@gmail.com on 23 Jul 2013 at 1:54

GoogleCodeExporter commented 9 years ago

Support for paired-end trimming has been in cutadapt for a while thanks to 
James' patch. I'm therefore closing this long-standing issue.

Original comment by marcel.m...@tu-dortmund.de on 6 Feb 2014 at 10:08

Changed state: Fixed