how to check peak quality of chip seq data

[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.

[repinementer]

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

[dawe]

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]

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