Jump to content

  • Log in with Facebook Log in with Twitter Log in with Windows Live Log In with Google      Sign In   
  • Create Account

Submit your paper to J Biol Methods today!
Photo
- - - - -

Free ChIP sequencing analysis software?


  • Please log in to reply
2 replies to this topic

#1 bioforum

bioforum

    Veteran

  • Super Administrators
  • PipPipPipPipPipPipPipPipPipPip
  • 164 posts
52
Excellent

Posted 20 October 2009 - 12:05 PM

Posted for Sara Jackson

Hi

Please suggest me online software for automated analysis of Chip-Seq data.

Thanks in advance.

#2 methylnick

methylnick

    Veteran

  • Global Moderators
  • PipPipPipPipPipPipPipPipPipPip
  • 262 posts
5
Neutral

Posted 25 October 2009 - 02:52 PM

Hi Sara,

sorry i haven't responded, I am not that familiar with the software that is available.

We are starting to think about doing some ChIP-seq but it appears you are ahead of us for sure.

Peter Park's group at Harvard would be a good contact point as I know they have been playing with a lot of ChIP-seq data.

CisGenome is a mapping software package that can do SOLiD and GAII sequence data sets I was told about but I haven't used it before and it's free.

Hope this gives you some pointers into the right direction.

Nick

All comments and communication are my own personal ones, and are not tied to any of my affiliations. 


#3 username

username

    member

  • Active Members
  • Pip
  • 6 posts
0
Neutral

Posted 30 October 2009 - 06:40 AM

Hi Sara,

sorry i haven't responded, I am not that familiar with the software that is available.

We are starting to think about doing some ChIP-seq but it appears you are ahead of us for sure.

Peter Park's group at Harvard would be a good contact point as I know they have been playing with a lot of ChIP-seq data.

CisGenome is a mapping software package that can do SOLiD and GAII sequence data sets I was told about but I haven't used it before and it's free.

Hope this gives you some pointers into the right direction.

Nick



I think CisGenome starts with the analysis after mapping. So you start with detection of peaks, motif finding... In addition, CisGenome has a graphic user interface on windows, and is a bit easyer to use. There are a lot of freely available tools, like MAQ or Bowtie for mapping, MACS, FindPeaks, Quest... for peak finding.
Good luck




Home - About - Terms of Service - Privacy - Contact Us

©1999-2013 Protocol Online, All rights reserved.