Total Tags / Tags after filtering

[Henry Paik]

Hello MACS,

In peaks.xls file, one of the MACS output files, I could find "total
tags in treatment" and "tags after filtering in treatment" as well as
"total tags in control" and "tags after filtering in control".

And in the Genome Biology MACS paper, it reads "Peak detection -- For
experiments with a control, MACS linearly scales the total control tag
count to be the same as the total tag count." Is this still true with
1.4.0rc2?

I am wondering which number that MACS is using for the scaling. "total
tags in treatment" or "tags after filtering in treatment"? (I think
"tags after filtering" number, but want to make sure)

In my experiment, I got more reads in the control than in the sample.
Would MACS use the number in the sample to linearly scale the control
to sample?

I am using
$ macs14 --version
macs14 1.4.0rc2 20110214 (Valentine)

Thanks!

- Henry

[Tao Liu]

Hi Henry,

I will use inline reply.

On May 12, 2011, at 10:10 AM, Henry Paik wrote:

> And in the Genome Biology MACS paper, it reads "Peak detection -- For
> experiments with a control, MACS linearly scales the total control tag
> count to be the same as the total tag count." Is this still true with
> 1.4.0rc2?

Yes. But in 1.4rc2, I made some adjustments. You can find the following in
ChangeLog:

* pvalue and FDR fixes (Thanks to Prof. Zhiping Weng)

By default, MACS will now scale the smaller dataset to the bigger
dataset. For instance, if IP has 10 million reads, and Input has 5
million, MACS will double the lambda value calculated from Input
reads while calling BOTH the positive peaks and negative
peaks. This will address the issue caused by unbalanced numbers of
reads from IP and Input. If --to-small is turned on, MACS will
scale the larger dataset to the smaller one. So from now on, if d
is fixed, then the peaks from a MACS call for A vs B should be
identical to the negative peaks from a B vs A.

> I am wondering which number that MACS is using for the scaling. "total
> tags in treatment" or "tags after filtering in treatment"? (I think
> "tags after filtering" number, but want to make sure)

MACS uses 'tags after filtering', so you are right.

> In my experiment, I got more reads in the control than in the sample.
> Would MACS use the number in the sample to linearly scale the control
> to sample?

In your case, by default, it will scale ChIP data up to match control data. If you
specify '--to-small', it will scale control data down to match ChIP data.

Best,
Tao

[Henry Paik]

Thanks for your clear explanation!

- Henry

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