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Free ChIP sequencing analysis software?


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#1 bioforum

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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

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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

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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




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