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handling partial adapter spanning 5' to 3' #152
I have this case where, I wanted to trim an adapter
I intentionally left a gap in the above sequence for you to easily spot the portion of the adapter sequence. What I wanted in this case is, the entire read needs to be removed. The command that I have used didn't handle this case:
You can also see in my above command that I am using fastx_clipper to remove any reads that contained Ns, a feature if inherently present in cutadapt would be great.
I would be very happy if you could help me with a solution to handle this case.
Thanks a lot! :)
Interesting, do you have an idea why the adapters are degraded in such a way? Just to make sure: Is it correct that the untrimmed read starts with
I’m travelling at the moment and cannot test it, but if the degraded adapter is always
An option to discard reads that contain
They are the reads from SOLiD 5500XL
I just saw that cutadapt already has this feature. Using
No, it could be any of these. I've tested these scenarios.
When you use the
To complete this case, you could also add the
This essentially mean that you are (almost) removing the entire read, which can then be filtered with cutadapt's
What are your comments about this ?
You are right, that functionality already exists. I forgot about it because it was contributed externally.
I won’t use the exact syntax you suggested (because options are allowed to be only single characters), but the functionality will be what you described.
Thank you for your suggestion! Late, and possibly no longer relevant for you, but it is now possible to specify that a 3' adapter should be found also when it occurs partially at the 5' end. Please see the new section in the documentation.
This will be in Cutadapt 1.18.