about paired-end reads

[qwzhang]

HI MACS experts:

We have some paired-end ChIP-seq data. Are there any special strategies to use MACS on paired-end reads? Does MACS only consider each end of the paired-end reads as single-end reads and then call the peaks by the "single-end" reads? Is there any improvement for the paired-end reads?

Thanks

[Aengus Stewart]

Hi,


Unfortunately I have an old project that hasnt quite finished with a large amount of data which was processed with 1.3.7.1. I now have a "final" dataset which
needs to get added to the other results and I need to process it in exactly the same way with 1.3.7.1 for consistency.

Also unfortunately our farm is now running redhat 6 and having downloaded 1.3.7.1 again, I get the following error

bioadmin@leibniz bin]$ ./macs
Traceback (most recent call last):
File "./macs", line 34, in <module>
from MACS.OptValidator import opt_validate
ImportError: No module named MACS.OptValidator

Sorry I havent a clue about python!

Is there any chance someone can point me in the right direction to fix this?


Regards
Aengus

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[guoshicheng2005]

Dear ALL：

 

I have several question about Macs：

1，why 36 nt tags just  take 6 bytes in memory ？

2，Is there any evaluation of the influence to the result for different Band with?

3,  how to judge whether it is a peak, i can't find the statistic model for this question?

 

Your help will be greatly appreciated.

Best wishes!

Yours Shicheng Guo

 

2012-08-19

---

Your Sincerely Alexander(Alex)

 

Ministry of Education Key Laboratory of Contemporary Anthropology
School of Life Sciences, Fudan University
220 Handan Road
Shanghai, China 200433
Phone:15216760764
Office Tel:021-55664474
E-mail: guoshic...@yeah.net

 

[Aengus Stewart]

Sorry problem fixed. Simple PYTHONPATH issue.

Note to self. Dont send emails at end of day when fed up.


Regards
Aengus

[Tao Liu]

Hi Shicheng,

On Aug 19, 2012, at 1:43 AM, guoshicheng2005 <guoshic...@yeah.net> wrote:

> 1，why 36 nt tags just take 6 bytes in memory ？

You have to read my source code if you want to know technical detail :)

> 2，Is there any evaluation of the influence to the result for different Band with?

Band width is only used to find optimal fragment size. Then fragment size will have influence on the final peaks. I would rather tweak fragment size by --shift-size directly, rather than playing with bandwidth setting.

> 3, how to judge whether it is a peak, i can't find the statistic model for this question?

You have to read the MACS paper published in 2008. If you are talking about general peak calling, you'd better search for some review papers on ChIP-seq peak calling.

Best wishes,

Tao Liu

Research Fellow
Dept of Biostats and Comp Bio, DFCI / HSPH
450 Brookline Ave., Boston, MA 02215
(O) 617-582-7769