Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
bwa sampe bam input avinash Bioinformatics 8 09-18-2012 09:21 AM
ChIP-Seq: ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expre Newsbot! Literature Watch 0 05-19-2011 03:50 AM
ChIP-Seq: ChIP-chip versus ChIP-seq: Lessons for experimental design and data analysi Newsbot! Literature Watch 0 03-02-2011 03:50 AM
18bp DNA contaminant in ChIP input sample? sinapius Sample Prep / Library Generation 0 02-09-2011 12:39 PM
ChIP-Seq: ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip dat Newsbot! Literature Watch 0 05-13-2010 03:00 AM

Thread Tools
Old 07-21-2010, 02:19 PM   #1
Junior Member
Location: usa

Join Date: Jul 2010
Posts: 1
Default Can I randomly sampe from ChIP seq input

I have a problem for peak calling. Could anyone help me?
After bowtie, I am using MACS to call peaks. There are 12 million unique reads in input, but there are only 4 million unique reads in my IP. The number of peaks called by MACS is not as high as I expected based on ChIP-chip. I am guessing some of the peaks may be masked because of the more reads in input. How could I solve this problem? Any suggestion?

I plan to randomly select comparable number of reads from input and call peak again. Does it make sense to do so? If it does, how could I do the job? I do not know how to do it.
skying is offline   Reply With Quote

chip seq, input, peak, random

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 01:47 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO