CLIP/RIP-seq peak finding

Mali Salmon · 02-12-2012, 03:12 AM

A question to all users that run CLIP/RIP-seq and then try to find peaks in their data.
Since I couldn't find any specific tool for finding peaks in RNA-based data, I have decided to use the classical ChIP-seq tools (the logic is the same I think).
I align reads to the genome (I don't really care about junction reads), and then run one of the ChIP-seq tools such as MACS.
I would like to hear about the parameters people use when they run ChIP-seq tools on CLIP/RIP-seq data. For example many of the ChIP-seq tools use the "genome size" for random expectation calculations, and different genome sizes give different output.
Do you use the transcriptome size or genome size when trying to find significant peaks?
Any other issues that should be taken care of?
Thanks
Mali

ETHANol · 02-12-2012, 03:28 AM

I am by no means the expert on this topic but I have been reading about it a little here and there the last few days. From what I have read, using a ChIP-seq data analysis pipeline results in the identification of many false positives. I haven't seen any well documented workflows but you may want to check out this thread:
http://seqanswers.com/forums/showthread.php?t=14775

Mali Salmon · 02-12-2012, 03:38 AM

Thanks ETHANol for your reply. Can you explain more why ChIP-seq pipeline is not suitable for RNA-based data, what is the reason for the high false-positive rate?
I have RNA-IP sample and RNA-Input and would like to find enriched peaks. The idea is basically the same as with ChIP-seq.
Mali

ETHANol · 02-12-2012, 03:41 AM

I wish I could give you an answer but at this point I would probably just be polluting the forum with half-truths. Hopefully, someone with more experience on the topic will chime in.

monique1 · 04-24-2012, 07:37 PM

We are interested in finding RNAs that interact with specific regions of chromatin. Do you know if there is a technique out there for this? Thanks.

mudshark · 04-25-2012, 03:29 AM

a) either you have a protein specifically associating with these loci, then use an IP followed by RNASeq

b) otherwise the only regions in chromatin that can be purified so far (i know many people that tried others and failed) are telomers
http://www.cell.com/abstract/S0092-8674(08)01520-1

c) or do you work in yeast? then there might be other options.

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
RIP-Seq	SeeElle	RNA Sequencing	14	01-22-2020 04:16 AM
Rip-seq	Bioinfo83	Academic/Non-Profit Jobs	0	10-13-2011 12:36 PM
More information on RIP-seq	sciencewu	Epigenetics	0	08-30-2011 04:18 AM
Peak finding tools	vaibhav_jain	Bioinformatics	3	07-28-2011 03:15 AM
Peak finding with MACS: Questions on # of reads and "strand bias"	jjw14	Bioinformatics	0	07-29-2010 07:17 AM

02-12-2012, 03:12 AM	#1
Mali Salmon Member Location: UK Join Date: Jul 2008 Posts: 24	CLIP/RIP-seq peak finding A question to all users that run CLIP/RIP-seq and then try to find peaks in their data. Since I couldn't find any specific tool for finding peaks in RNA-based data, I have decided to use the classical ChIP-seq tools (the logic is the same I think). I align reads to the genome (I don't really care about junction reads), and then run one of the ChIP-seq tools such as MACS. I would like to hear about the parameters people use when they run ChIP-seq tools on CLIP/RIP-seq data. For example many of the ChIP-seq tools use the "genome size" for random expectation calculations, and different genome sizes give different output. Do you use the transcriptome size or genome size when trying to find significant peaks? Any other issues that should be taken care of? Thanks Mali

02-12-2012, 03:28 AM	#2
ETHANol Senior Member Location: Western Australia Join Date: Feb 2010 Posts: 308	I am by no means the expert on this topic but I have been reading about it a little here and there the last few days. From what I have read, using a ChIP-seq data analysis pipeline results in the identification of many false positives. I haven't seen any well documented workflows but you may want to check out this thread: http://seqanswers.com/forums/showthread.php?t=14775 __________________ -------------- Ethan

02-12-2012, 03:41 AM	#4
ETHANol Senior Member Location: Western Australia Join Date: Feb 2010 Posts: 308	I wish I could give you an answer but at this point I would probably just be polluting the forum with half-truths. Hopefully, someone with more experience on the topic will chime in. __________________ -------------- Ethan

02-12-2012, 03:38 AM	#3
Mali Salmon Member Location: UK Join Date: Jul 2008 Posts: 24	Thanks ETHANol for your reply. Can you explain more why ChIP-seq pipeline is not suitable for RNA-based data, what is the reason for the high false-positive rate? I have RNA-IP sample and RNA-Input and would like to find enriched peaks. The idea is basically the same as with ChIP-seq. Mali

04-24-2012, 07:37 PM	#5
monique1 Junior Member Location: new york Join Date: Apr 2012 Posts: 1	We are interested in finding RNAs that interact with specific regions of chromatin. Do you know if there is a technique out there for this? Thanks.

04-25-2012, 03:29 AM	#6
mudshark Senior Member Location: Munich Join Date: Jan 2009 Posts: 138	a) either you have a protein specifically associating with these loci, then use an IP followed by RNASeq b) otherwise the only regions in chromatin that can be purified so far (i know many people that tried others and failed) are telomers http://www.cell.com/abstract/S0092-8674(08)01520-1 c) or do you work in yeast? then there might be other options.