What does skew detection mean? mcf_fastq

[pepperoni]

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

[earonesty]

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.

[pepperoni]

Thank you earonesty, which percentage would you recommend?