I´m trying to analyze Chip-SEq Data from Ion-Torrent using Peak
Calling/MACS. I have some questions:
· How do I establish the Tag size? The median of size reads
in my data are 156pb, the max 306?
· Bandwidht: is the sonication size?
Thanks in advance
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The median size is probably fine, unless the distribution of size is
highly skewed or dispersed, but even then you have to start somewhere.
have always thought this post on the MACS google group was good
With short tags, original read seemed to map in entirety most of the
time, so using the original query length was a simple way to go about
it. With longer reads, using the actual length of the alignment (what
MACS will be considering, after all) makes a great deal of sense, but
may be unnecessary. Still - good to know about if you want to test it
And it looks like others are still agreeing with the basic approach
(start of with the mean of the original sequence):
Bandwidth should be set to half the sonication size - the authors
that an estimate is also fine.
Use the shifting model.
And set the genome size accurately - using the actual size of the
reference mapped against.
More details are in the original MAC publication & manual & google