Use fastq-mcf with methylation data

[GoogleCodeExporter]

I'm using the fastq-mcf (1.04.662) in my pipeline to filter adaptors and trim 
reads by quality.

I have used it for a methylation sequencing run and I didn't change the skew 
parameter, I left the default parameter -k=2.

I would like to know if would be better to re-run with k=0, just like in the 
help, what is the impact in the reads with -k=2 ?

I would like to know what the -k parameter does to the sequences, it will trim 
them ?

I look at some fastq-mcf reports and show the below messages for the positions 
from 1 to 49:

Within-read Skew: Position XXX from the start of reads is skewed!
Within-read Skew: Position XXX from the end of reads is skewed!

what this means ? This positions were trimmed ?

Best regards,

Milton

Original issue reported on code.google.com by yutak...@gmail.com on 7 May 2015 at 2:53

[GoogleCodeExporter]

i would re-run with -k 0 ... skew is really a problem that doesn't happen as 
much with newer sequencers and -k=0 should probably be the new default

Original comment by earone...@gmail.com on 26 Jun 2015 at 2:23

[GoogleCodeExporter]

my doubt is what the software does with the skewed position(s) in the read, are 
they removed ?

it could remove methylated regions ?

Thanks

Original comment by yutak...@gmail.com on 26 Jun 2015 at 2:31