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Old 06-09-2011, 04:54 AM   #14
Location: uk

Join Date: Jun 2010
Posts: 38

Originally Posted by Jose Blanca View Post
You can not use the --qual_thrshold parameter for long reads (sanger or 454). I have to explain that in the documentation a little. For the long reads we trim the bad quality regions by using lucy so the parameter to change would be lucy_error. qual_threshold is used by the short reads quality trimmer.
Hi Jose
I am trying to do quality trimming and filtering 454 reads. The adaptors and primers and barcode sequences are already removed.I am not allowed to specific minimum quality threshold to clean bad quality reads. I don't understand why? How does it do quality trimming. Sorry I could not get documentation of clean_reads. And when i specify option -only_3_end True, it gave me error not compatible with platform. So does it mean it trims from 5' and 3' prime ends.

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