SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
p-value for peak-calling using MACS ywlim Bioinformatics 8 08-08-2013 02:27 AM
MACS: output of MACS as an control file? jaaker Bioinformatics 0 08-22-2012 09:09 AM
peak calling for TSS detection in bacteria pole_sana Bioinformatics 1 07-19-2012 04:21 AM
Merging MACS Peak analysis +/- duplicates? Combo Epigenetics 8 12-21-2011 07:07 AM
Peak finding with MACS: Questions on # of reads and "strand bias" jjw14 Bioinformatics 0 07-29-2010 06:17 AM

Reply
 
Thread Tools
Old 07-24-2014, 06:39 PM   #1
Ayyappa_kumar
Member
 
Location: India

Join Date: Feb 2014
Posts: 14
Thumbs up Peak detection using MACS

I have performed peak detection on my sample data which has one treatment sample and once control sample, It has resulted me with four lists: a) NA_Negative peaks, b) NA_Peaks.bed c) NA_peaks.xls d) NA_summits.bed.

I have used the NA_Peaks.bed for motif detection, but am not sure regarding my selection? And also does NA_Negative peaks list represents the peaks obtained from the -ve Strand? Any suggestions will be really helpful !!
Ayyappa_kumar is offline   Reply With Quote
Old 07-25-2014, 01:39 AM   #2
paolo.kunder
Member
 
Location: Milano, Italy

Join Date: Aug 2011
Posts: 93
Default

In MACS README file is well explained:

http://liulab.dfci.harvard.edu/MACS/00README.html

NAME_peaks.xls is a tabular file which contains information about called peaks.

NAME_peaks.bed is BED format file which contains the peak locations.

NAME_summits.bed is in BED format, which contains the peak summits locations for every peaks. The 5th column in this file is the summit height of fragment pileup.

NAME_negative_peaks.xls is a tabular file which contains information about negative peaks. Negative peaks are called by swapping the ChIP-seq and control channel.
paolo.kunder is offline   Reply With Quote
Old 07-25-2014, 04:30 AM   #3
Ayyappa_kumar
Member
 
Location: India

Join Date: Feb 2014
Posts: 14
Default

Thanks for your reply !!!

So one should use peaks.bed file for motif detection, please let me know if am not wrong.
Ayyappa_kumar 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 04:48 AM.


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