SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
ChIP-Seq: AREM: Aligning Short Reads from ChIP-Sequencing by Expectation Maximization Newsbot! Literature Watch 0 11-01-2011 04:20 AM
ChIP-Seq: ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expre Newsbot! Literature Watch 0 05-19-2011 02:50 AM
ChIP-Seq: ChIP-chip versus ChIP-seq: Lessons for experimental design and data analysi Newsbot! Literature Watch 0 03-02-2011 02:50 AM
ChIP-Seq: Processing and analyzing ChIP-seq data: from short reads to regulatory inte Newsbot! Literature Watch 0 09-24-2010 02:10 AM
ChIP-Seq: ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip dat Newsbot! Literature Watch 0 05-13-2010 02:00 AM

Reply
 
Thread Tools
Old 07-26-2012, 02:22 AM   #1
TheStudent
Member
 
Location: Europe

Join Date: Nov 2011
Posts: 10
Default Enough reads in Chip-Seq?

Dear Community,

I am new to ChIP-seq so please be gentle.

Analyzing ChIP-seq data - public and from my collaborators - I realized that the minimum of reads is varying very much - NCBI's minimum to submit ChIP-seq is 1 million short reads I heard and I saw published data with even less than that.

Looking at the distribution of reads in UCSC browser (by uploading the .bam files) it looks very random over the whole genome, sometimes reads are stacking up a bit.

Here the questions:

A) Should you normally be able to spot peaks visually?
The peak callers take into account fragment size as well I suppose, but usually should you be able to see distinct peaks by eye?

B) If not - if it looks all over the genome, does that mean that there are not enough reads to detect peaks reliable?

C) How many reads would you recommend minimum for Illumina GAIIx - read length 37 - 42nt for TFs like Myc-n or NFkB-p50?

Thank you very much
TheStudent is offline   Reply With Quote
Old 07-26-2012, 03:00 AM   #2
ffinkernagel
Senior Member
 
Location: Marburg, Germany

Join Date: Oct 2009
Posts: 110
Default

A) Very much so.
B) Either that or your ChIP did not work.
C) Very much depends on the antibody, and the portion of the genome covered by your factor. For those two, I'd start at minimum of 20 million reads, but I'd expect a need to increase the depth.
ffinkernagel is offline   Reply With Quote
Old 07-26-2012, 03:22 AM   #3
TheStudent
Member
 
Location: Europe

Join Date: Nov 2011
Posts: 10
Default

thanks,

It is expected that those factors bind a lot in the genome
TheStudent is offline   Reply With Quote
Old 07-26-2012, 03:34 AM   #4
ffinkernagel
Senior Member
 
Location: Marburg, Germany

Join Date: Oct 2009
Posts: 110
Default

Indeed - but then at least for myc I know that the antibody is pretty decent.
ffinkernagel is offline   Reply With Quote
Reply

Tags
chip-seq, coverage, reads

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 09:16 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO