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?
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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Aengus Stewart Tel: +44 (0)20 7269 3679
Head of Bioinformatics and BioStatistics
CRUK London Research Institute
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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: guoshicheng2...@yeah.net
> 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
-- -----------------------------------------------------------------------
Aengus Stewart Tel: +44 (0)20 7269 3679
Head of Bioinformatics and BioStatistics
CRUK London Research Institute
Lincoln's Inn Fields, Holborn, London, WC2A 3LY, UK
-----------------------------------------------------------------------
This electronic message contains information which may be privileged and
confidential. The information is intended to be for the use of the
individual(s) or entity named above. Be aware that any third party
disclosure, distribution, copying or use of this communication, without
prior permission, is strictly prohibited.
NOTICE AND DISCLAIMER
This e-mail (including any attachments) is intended for the above-named person(s). If you are not the intended recipient, notify the sender immediately, delete this email from your system and do not disclose or use for any purpose.
We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to ensure that this email and attachments are free from any virus, but it remains your responsibility to ensure that viruses do not adversely affect you. Cancer Research UK
Registered charity in England and Wales (1089464), Scotland (SC041666) and the Isle of Man (1103)
A company limited by guarantee. Registered company in England and Wales (4325234) and the Isle of Man (5713F).
Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD.
On Aug 19, 2012, at 1:43 AM, guoshicheng2005 <guoshicheng2...@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
