SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Is it possible to convert a SNP.txt to a bed file or get a SNP.bed from samtools? Ling Bioinformatics 7 04-02-2015 06:17 AM
Is there a BED file format validator? Does a BED file have to be sorted position? LauraSmith Bioinformatics 3 05-21-2013 11:54 AM
Eland to Bed __sequence Illumina/Solexa 0 06-08-2011 04:07 AM
bed file???? semna RNA Sequencing 0 03-07-2011 04:41 AM
.baf 2 BED JohnK SOLiD 3 04-13-2010 10:45 AM

Reply
 
Thread Tools
Old 02-07-2011, 12:48 AM   #1
khb
Member
 
Location: Oslo

Join Date: Dec 2010
Posts: 15
Default Missing strand _peaks.bed

Hi
I've tried to analyze my data with MACS, and want the file _peaks.bed that MACS gives. Does anyone know how to know which strand each peak is on? The file only contains
chrom start stop name score
Thanks

Last edited by khb; 02-07-2011 at 12:59 AM.
khb is offline   Reply With Quote
Old 02-07-2011, 01:46 AM   #2
ffinkernagel
Senior Member
 
Location: Marburg, Germany

Join Date: Oct 2009
Posts: 110
Default

The answer to your question is 'mu'.

A chipseq peak has no strandedness... in theory, you should only see reads of one strand on one, and of the other strand on the other side, crossing over wherever your protein bound the chromatin (since fragments starting further down on the same strand would not have a protein bound, and would not be visible after the chip). In practice, it's not that clear cut. Nevertheless, the peak does not have a strand.
ffinkernagel is offline   Reply With Quote
Old 02-07-2011, 02:58 AM   #3
khb
Member
 
Location: Oslo

Join Date: Dec 2010
Posts: 15
Default

Of course. Thanks
khb is offline   Reply With Quote
Old 08-14-2011, 10:40 AM   #4
rossignol
Junior Member
 
Location: Finland

Join Date: Aug 2011
Posts: 1
Default

Hi,

I see the point about peaks not having a strand. What should I then submit to HOMER when doing motif analysis? HOMER expects to get a peak file in bed format, with the last column being +/- for the strand of the peak.
rossignol 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 12:57 PM.


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