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alexstaj / cutadapt

Automatically exported from code.google.com/p/cutadapt
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distinguish multiple adapters #62

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
I'm using cutadapt to sort reads based on the adapter (in a 4C experiment). 

I've currently hacked the info-file to print the exact adapter sequence, as 
opposed to the adapter sequence observed (including mismatches - harder to map 
back to the original adapter list)

It would be nice if this was a real feature, maybe even with the option to sort 
the reads into separate files based on the adapter sequences.

btw - excellent tool
Mark

Original issue reported on code.google.com by mark.fie...@gmail.com on 7 May 2013 at 12:01

GoogleCodeExporter commented 9 years ago 
Yes, good idea. I’ve also heard from some other people that they were (at 
least trying to) use cutadapt for de-multiplexing. I’m busy with other things 
right now, but plan to get back to cutadapt development in a few weeks.

Original comment by marcel.m...@tu-dortmund.de on 7 May 2013 at 3:40

GoogleCodeExporter commented 9 years ago 
Yes, it would be great to have this information.
Maybe, as a quick fix, just add a column in the info file that named the 
adapter found in each read.

great tool !

Seb

Original comment by seb.th...@gmail.com on 28 Jan 2014 at 2:45

GoogleCodeExporter commented 9 years ago 
I'm just working on this. I've got two different options: Either I add a column 
with the name of each adapter (adapters can be named, as in '-a 
adaptername=AGGACT') or a column that just contains the adapter sequence. What 
would be more useful? Note that one could set the name of the adapter to be the 
same as its sequence ... (-a AGGACT=AGGACT).

Original comment by marcel.m...@tu-dortmund.de on 6 Feb 2014 at 10:04

GoogleCodeExporter commented 9 years ago 
Both sound fine to me - with the name=CGTAGC option a little more flexible. 

And, while I'm at it (:)) - adapter identification is usually followed by 
sorting the sequences into separate files, so, that would be a very nice 
feature to have as well.

cheers, Mark

Original comment by mark.fie...@gmail.com on 7 Feb 2014 at 7:10

GoogleCodeExporter commented 9 years ago 
A column with the adapter name will be just fine !
Seb

Original comment by seb.th...@gmail.com on 10 Feb 2014 at 6:24

GoogleCodeExporter commented 9 years ago 
Ok, just committed a change that adds a 'name' column to the info file! No 
built-in demultiplexing so far ... I'll leave the issue open for a while in 
case I find a simple way to implement that.

Original comment by marcel.m...@tu-dortmund.de on 14 Feb 2014 at 9:12

GoogleCodeExporter commented 9 years ago 
Nice! Thanks.

btw - I did not want to seem overly eager - I'm happy as is.

Original comment by mark.fie...@gmail.com on 15 Feb 2014 at 6:44

GoogleCodeExporter commented 9 years ago 
Demultiplexing is available in cutadapt 1.7.

Original comment by marcel.m...@tu-dortmund.de on 8 Mar 2015 at 9:36