SICER (histone ChIP-Seq)

rebrendi · 02-22-2012, 05:58 AM

Hello,

I am trying to use SICER to extract regions of histone modification enrichment. I am expecting to get regions of size ~100 Kb, but only getting ~1 Kb regions with this program (with MAQ it was even worse). Any suggestions how to tinker with the SICER parameters, or any other thoughts?

Thanks!

rebrendi · 02-23-2012, 05:56 AM

if there are no experts in SICER here, may be one can suggest another program for broad ChIP-Seq peaks?

kopi-o · 02-23-2012, 09:46 AM

Back when I was working with this kind of thing, I used CCAT and SICER.

Now, there are some other alternatives as well. I haven't tried any of these, so I'll just provide some links for your information:

- PeakRanger. Claims to work well for diffuse profiles. http://ranger.sourceforge.net/

- LPCHP. Very recent publication: Signal analysis for genome wide maps of histone modifications measured by ChIP-seq. (http://www.ncbi.nlm.nih.gov/pubmed/2...?dopt=Abstract)

- A benchmark paper oriented towards epigenetics modification ChIP-seq: Picking ChIP-seq peak detectors for analyzing chromatin modification experiments. (http://www.ncbi.nlm.nih.gov/pubmed/2...?dopt=Abstract)

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02-22-2012, 05:58 AM	#1
rebrendi ng Location: LA Join Date: May 2008 Posts: 78	SICER (histone ChIP-Seq) Hello, I am trying to use SICER to extract regions of histone modification enrichment. I am expecting to get regions of size ~100 Kb, but only getting ~1 Kb regions with this program (with MAQ it was even worse). Any suggestions how to tinker with the SICER parameters, or any other thoughts? Thanks!

02-23-2012, 05:56 AM	#2
rebrendi ng Location: LA Join Date: May 2008 Posts: 78	if there are no experts in SICER here, may be one can suggest another program for broad ChIP-Seq peaks?

02-23-2012, 09:46 AM	#3
kopi-o Senior Member Location: Stockholm, Sweden Join Date: Feb 2008 Posts: 319	Back when I was working with this kind of thing, I used CCAT and SICER. Now, there are some other alternatives as well. I haven't tried any of these, so I'll just provide some links for your information: - PeakRanger. Claims to work well for diffuse profiles. http://ranger.sourceforge.net/ - LPCHP. Very recent publication: Signal analysis for genome wide maps of histone modifications measured by ChIP-seq. (http://www.ncbi.nlm.nih.gov/pubmed/2...?dopt=Abstract) - A benchmark paper oriented towards epigenetics modification ChIP-seq: Picking ChIP-seq peak detectors for analyzing chromatin modification experiments. (http://www.ncbi.nlm.nih.gov/pubmed/2...?dopt=Abstract)