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Old 10-06-2016, 04:23 AM   #3
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
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Quote:
Originally Posted by SDPA_Pet View Post
Hello, does anyone know the cutoff of trimming length. I have Illumina data from 2X150bp and 2X250bp sequencing. I'd like to trim them. I set the Q score to 30. How about length? What is the cutoff do you normally use?

For example, for 2X150bp data, should I discard all the reads short than 75bp or 100bp? How about 2X250 bp? I just want know the cutoff people usually use? Phred score >30 is normally use. I am not sure about the length.

Thanks
Q30 is an unnecessarily high cutoff, if all you are doing is aligning to a reference. You could omit trimming based on quality altogether in this case.

If you were going to do de novo assembly then you may want to trim at Q20-25.

If you are seeing a large amount of data getting trimmed then there may be some issue with your data that you would want to investigate further.
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