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alexstaj / cutadapt

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Trim fixed number of bases from 5' end #74

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
Feature request: option to trim a fixed number (user-defined) of bases from the 
5' end of every read. This is useful for RNAseq where the first bases of the 
read reflect the RT priming oligo and have a high 'error' rate.

Original issue reported on code.google.com by jkgren...@gmail.com on 13 May 2014 at 8:48

GoogleCodeExporter commented 9 years ago 
This would be easy to implement, but I need to decide whether it is worth 
adding this feature since there are already so many options. Will think about 
it.

Original comment by marcel.m...@tu-dortmund.de on 15 May 2014 at 10:36

GoogleCodeExporter commented 9 years ago 
Thanks for your consideration! And the more I read about trimming the 5' end of 
reads for RNAseq data, the less critical I think it is. I'll do some testing 
using other software that allows such fixed-length trimming to see if it makes 
a difference in the final analysis.

Original comment by jkgren...@gmail.com on 16 May 2014 at 12:52

GoogleCodeExporter commented 9 years ago 
I've just implemented a new option named --cut, which can be abbreviated to -u. 
It allows one to trim a given number of bases from the beginning or end of each 
read. See the section in the README:
https://github.com/marcelm/cutadapt/#removing-bases-from-the-beginning-or-end-of
-each-read

It's even a bit faster than fastx_trimmer with the -f option.

Original comment by marcel.m...@tu-dortmund.de on 27 May 2014 at 4:14

GoogleCodeExporter commented 9 years ago 
Thank you for this enhancement!

Original comment by jkgren...@gmail.com on 27 May 2014 at 8:37

GoogleCodeExporter commented 9 years ago 
Hi, Is it possible to download v1.5 that includes the --cut option? What do I 
need to do to update to v1.5?
Thanks in advance!

Original comment by jkgren...@gmail.com on 18 Jun 2014 at 6:42

GoogleCodeExporter commented 9 years ago 
You can go to https://github.com/marcelm/cutadapt/ and click on the 'Download 
ZIP' button on the right-hand side in order to get the current development 
version. You will have to follow the installation instructions in the README, 
though.

Original comment by marcel.m...@tu-dortmund.de on 19 Jun 2014 at 12:41

GoogleCodeExporter commented 9 years ago 
Implemented in cutadapt 1.5, which was released today.

Original comment by marcel.m...@tu-dortmund.de on 5 Aug 2014 at 11:40