[Bioc-sig-seq] annotatePeakInBatch feature request

[Dario Strbenac]

Oops. I don't ever work with TF-seq, and I just read that it isn't strand specific. I was trying to make a commonly used example.

A less well known, but correct example would be meDIP-seq. The antibody picks up denatured, single stranded DNA, so you can get stranded peaks with this technique (if you have methylation on one strand, and not on the other).

---- Original message ----
>Date: Fri, 4 Jun 2010 11:11:28 -0400
>From: "Zhu, Julie" <Julie.Zhu at umassmed.edu>  
>Subject: Re: [Bioc-sig-seq] annotatePeakInBatch feature request  
>To: "D.Strbenac at garvan.org.au" <D.Strbenac at garvan.org.au>, "bioc-sig-sequencing at r-project.org" <bioc-sig-sequencing at r-project.org>
>
>Hi Dario,
>
>If possible, could you please share your insight on the use case for
>distinguishing peaks at + strand from those at - strand? Thanks!
>
>I have several deadlines coming next week. I will try to work on the new
>feature the week after. Thanks!
>
>Best regards,
>
>Julie
>
>
>*******************************************
>Lihua Julie Zhu, Ph.D
>Research Associate Professor
>Program in Gene Function and Expression
>Program in Molecular Medicine
>University of Massachusetts Medical School
>364 Plantation Street, Room 613
>Worcester, MA 01605
>508-856-5256
>http://www.umassmed.edu/pgfe/faculty/zhu.cfm
>
>
>
>On 6/3/10 11:26 PM, "Dario Strbenac" <D.Strbenac at garvan.org.au> wrote:
>
>> Hi,
>> 
>> Would it be possible to have an extra choice for the PeakLocForDistance option
>> of the annotatePeakInBatch function ? A choice that uses the start if the peak
>> is on the + strand, and end if the peak is on the - strand (if the peaks have
>> a strand) ?
>> 
>> --------------------------------------
>> Dario Strbenac
>> Research Assistant
>> Cancer Epigenetics
>> Garvan Institute of Medical Research
>> Darlinghurst NSW 2010
>> Australia
>> 
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>> 
>
>