SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Odd MACS Warning jrmmhughes Bioinformatics 3 07-17-2016 08:57 PM
p-value for peak-calling using MACS ywlim Bioinformatics 8 08-08-2013 03:27 AM
MACS version 1.3.0 versus MACS version 1.4.0 neetu Bioinformatics 1 11-24-2011 04:13 AM
MACS SAMfiles khb Bioinformatics 2 12-19-2010 10:37 AM
MACS peaks VeenaV Bioinformatics 2 11-10-2010 09:46 AM

Reply
 
Thread Tools
Old 02-01-2011, 11:24 AM   #1
iros.barozzi
Junior Member
 
Location: Milan

Join Date: Jan 2010
Posts: 2
Default MACS 1.4.0beta

Hi,

I would like to share with all the MACS (http://liulab.dfci.harvard.edu/MACS/) users a revised version of the program.

Working with SAM files as input for this last MACS version, we noticed that in case the SAM file has thousands of lines representing unaligned reads at the beginning of it, the program crashes because it is not able to determine the length of the reads. I looked at the source code and modified the Parser.py in order to avoid this error. We tested it with some of our SAM files and it seems to work properly. I also modified the code in order to avoid this error with other input sources but I did not tested it yet. I attached the revised source code.

Iros Barozzi
PhD student
European Institute of Oncology, Milan (Italy)
Attached Files
File Type: gz MACS-1.4.0beta.iros.tar.gz (56.7 KB, 8 views)
iros.barozzi is offline   Reply With Quote
Old 02-02-2011, 01:37 PM   #2
seb567
Senior Member
 
Location: Québec, Canada

Join Date: Jul 2008
Posts: 260
Default

Quote:
Originally Posted by iros.barozzi View Post
Hi,

I would like to share with all the MACS (http://liulab.dfci.harvard.edu/MACS/) users a revised version of the program.

Working with SAM files as input for this last MACS version, we noticed that in case the SAM file has thousands of lines representing unaligned reads at the beginning of it, the program crashes because it is not able to determine the length of the reads. I looked at the source code and modified the Parser.py in order to avoid this error. We tested it with some of our SAM files and it seems to work properly. I also modified the code in order to avoid this error with other input sources but I did not tested it yet. I attached the revised source code.

Iros Barozzi
PhD student
European Institute of Oncology, Milan (Italy)
You should send a patch upstream, directly to the authors.

See the correponding authors in the Genome Biology paper (2008).
http://genomebiology.com/content/9/9/R137

-seb
seb567 is offline   Reply With Quote
Old 02-03-2011, 01:48 AM   #3
iros.barozzi
Junior Member
 
Location: Milan

Join Date: Jan 2010
Posts: 2
Default

I already tried but I had no reply. So I decided to post it here
iros.barozzi is offline   Reply With Quote
Old 05-19-2011, 02:38 PM   #4
ms5639
Junior Member
 
Location: New York, Manhattan

Join Date: May 2011
Posts: 1
Default Problem

Hello and thanks for this version! I have the same problem with my SAM files so I tried to use this but I get the following error message:

deepseq:~ schizas$ macs14 -t Data/MTmCmLs_5_1.sam
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.7/bin/macs14", line 336, in <module>
main()
File "/Library/Frameworks/Python.framework/Versions/2.7/bin/macs14", line 48, in main
options = opt_validate(prepare_optparser())
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/MACS14/OptValidator.py", line 143, in opt_validate
if options.keepduplicates != "auto" and options.keepduplicates != "all":
AttributeError: Values instance has no attribute 'keepduplicates'


Do you know how I can fix this?

Thank you
Michael Schizas
ms5639 is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 03:15 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO