SEQanswers

SEQanswers (http://seqanswers.com/forums/index.php)
-   Bioinformatics (http://seqanswers.com/forums/forumdisplay.php?f=18)
-   -   how to check peak quality of chip seq data (http://seqanswers.com/forums/showthread.php?t=5820)

repinementer 07-04-2010 07:20 PM

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.

repinementer 07-04-2010 07:30 PM

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

dawe 07-04-2010 10:48 PM

Quote:

Originally Posted by repinementer (Post 21305)
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 11:01 PM

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


All times are GMT -8. The time now is 11:42 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.