Hello Mónica,

The median size is probably fine, unless the distribution of size is highly skewed or dispersed, but even then you have to start somewhere. I have always thought this post on the MACS google group was good advice. 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 it may be unnecessary. Still - good to know about if you want to test it out.
https://groups.google.com/forum/#!searchin/macs-announcement/variable$20tag$20size/macs-announcement/Hhryd_jsVwY/0Fd9B_Z4goYJ

And it looks like others are still agreeing with the basic approach (start of with the mean of the original sequence):
https://groups.google.com/forum/#!topicsearchin/macs-announcement/tag$20size%7Csort:date%7Cspell:true/macs-announcement/-YD-WekWhIE

Bandwidth should be set to half the sonication size - the authors state 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 group:
http://liulab.dfci.harvard.edu/MACS/00README.html
http://www.biomedcentral.com/content/pdf/gb-2008-9-9-r137.pdf
https://groups.google.com/forum/#!forum/macs-announcement

Best,

Jen
Galaxy team

On 2/4/14 9:02 AM, Mónica Pérez Alegre wrote:

Hi everybody.

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

Regards

*?*If you have used the Services of the Genomics Unitof Cabimer, we would be grateful if you would give us a mention in future publications

*Mónica Pérez Alegre, PhD***

Genomics Unit

*CABIMER-CSIC***

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Parque Científico y Tecnológico Cartuja 93**

41092 Seville-SPAIN

Tlf:   +34 954 467 828**

Fax: +34 954 461 664**

*www.cabimer.es <http://www.cabimer.es/>*

*http://www.cabimer.es/web/es/unidades-apoyo/genomica*



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