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Old 02-08-2011, 08:07 AM   #3
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Originally Posted by tdoniger View Post
2. I tried using SeqClean -which actually manages to remove all the vector but does not provide a quality file. I could write some program that would produce a modified .qual file, but I was wondering if such a tool already exists.
Much Thanks,
Tirza Doniger

SeqClean includes a utility to create a new qual file which corresponds to your cleaned reads. The program is called 'cln2qual' and it is in the main seqclean directory. It takes as input the cleaning report generated by SeqClean (the .cln file) and your original .qual file. It outputs a new .qual file with appropriately trimmed (or excluded) qual scores.

Last edited by kmcarr; 02-08-2011 at 08:13 AM. Reason: Removed comments about read ordering in new qual file; mistaken about this.
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