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Old 06-27-2016, 04:11 AM   #126
fkrueger
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Location: Cambridge, UK

Join Date: Sep 2009
Posts: 614
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Hi Guorong,

I have added the option --trim-n now that should do just what you need. It also adds a few other features:

- Added option '--max_n COUNT' to remove all reads (or read pairs) exceeding this limit of tolerated Ns. In a paired-end setting it is sufficient if one read exceeds this limit. Reads (or read pairs) are removed altogether and are not further trimmed or written to the unpaired output.

- Enabled option '--trim-n' to remove Ns from both end of the reads. Does currently not work for RRBS-mode.

- Added new option '--max_length <INT>' which reads that are longer than <INT> bp after trimming. This is only advised for smallRNA sequencing to remove non-small RNA sequences.

- Replaced 'zcat' with 'gunzip -c' so that older versions of Mac OSX do not append a .Z to the end of the file and subsequently fail because the file is not present. Dah...

- Fixed a typo in adapter auto-detection warning message.

I have moved Trim Galore to Github where you can clone the latest development version: https://github.com/FelixKrueger/TrimGalore.
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