Posted for Sara Jackson
Hi
Please suggest me online software for automated analysis of Chip-Seq data.
Thanks in advance.
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2 replies to this topic
#2
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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
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
#3
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Posted 30 October 2009 - 06:40 AM
methylnick, on Oct 25 2009, 02:52 PM, said:
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
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
