how to check peak quality of chip seq data

repinementer · 07-04-2010, 06:20 PM

Hi guys is there any simple way to check both tag quality and peak quality of ChIPSEQ data

1.Tag and peak quality called by MACs (Transcription factors - ChIPseq)
2. Tag and Peak quality called by CCAT/GLITR (Histone modifications - ChIP seq)

PS:I have control to.

repinementer · 07-04-2010, 06:30 PM

Is it Hilbert curve?? or Sole-Search tool ??

dawe · 07-04-2010, 09:48 PM

Quote:

Originally Posted by repinementer

Hi guys is there any simple way to check both tag quality and peak quality of ChIPSEQ data

1.Tag and peak quality called by MACs (Transcription factors - ChIPseq)
2. Tag and Peak quality called by CCAT/GLITR (Histone modifications - ChIP seq)

PS:I have control to.

Can you better explain what you need? I mean, if you use MACS to compare an IP vs an Input, well, you should already have a list of significant peaks (with default parameters) and associated p-values, FDR and peak heights...

d

repinementer · 07-04-2010, 10:01 PM

ya but what is the optimal peak height??? or FDr???
Is there any statistical and graphical way to show the quality of data(peak heights or FDR)

Thanx

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07-04-2010, 06:20 PM	#1
repinementer Member Location: asia Join Date: Dec 2009 Posts: 80	how to check peak quality of chip seq data Hi guys is there any simple way to check both tag quality and peak quality of ChIPSEQ data 1.Tag and peak quality called by MACs (Transcription factors - ChIPseq) 2. Tag and Peak quality called by CCAT/GLITR (Histone modifications - ChIP seq) PS:I have control to. Last edited by repinementer; 07-04-2010 at 06:23 PM.

07-04-2010, 06:30 PM	#2
repinementer Member Location: asia Join Date: Dec 2009 Posts: 80	Is it Hilbert curve?? or Sole-Search tool ?? Last edited by repinementer; 07-04-2010 at 06:39 PM.

07-04-2010, 10:01 PM	#4
repinementer Member Location: asia Join Date: Dec 2009 Posts: 80	hi ya but what is the optimal peak height??? or FDr??? Is there any statistical and graphical way to show the quality of data(peak heights or FDR) Thanx