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Old 10-19-2011, 10:15 AM   #1
pepperoni
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Default What does skew detection mean? mcf_fastq

Hello, I am using fastq-mcf (http://code.google.com/p/ea-utils/wiki/FastqMcf) to trim my fastq files and there is an option for skew detection.
-k N sKew percentage causing trimming (2)

Does any one know what does that mean? shall I turn it off?
thanks

Last edited by pepperoni; 10-19-2011 at 10:19 AM.
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Old 12-10-2011, 10:22 PM   #2
earonesty
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Quote:
Originally Posted by pepperoni View Post
Hello, I am using fastq-mcf (http://code.google.com/p/ea-utils/wiki/FastqMcf) to trim my fastq files and there is an option for skew detection.
-k N sKew percentage causing trimming (2)

Does any one know what does that mean? shall I turn it off?
thanks
It means if there are less than (skew pct) A's in one cycle, then that WHOLE cycle is trimmed.

This effectively removes many artifacts of various unusual library preparations without disturbing normal preps.

The program tells you whether it detected or acted on skew... so you can safely leave it on, and not worry about it unless you see it detected in the output.

And even then, if it's detected consistently across an experiment, it shouldn't cause bias. But you might want to talk to the lab and find out why.
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Old 12-11-2011, 06:47 AM   #3
pepperoni
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Thank you earonesty, which percentage would you recommend?
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