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" <[email protected]> >Subject: Re: [Bioc-sig-seq] annotatePeakInBatch feature request >To: "[email protected]" <[email protected]>, >"[email protected]" <[email protected]> > >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" <[email protected]> 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 >> >> _______________________________________________ >> Bioc-sig-sequencing mailing list >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing >> > > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
