SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Applying Next-Gen Sequencing and Next-Gen Sequencing Data Analysis LifeScienceMarketing Events / Conferences 0 08-06-2012 07:21 AM
PubMed: miRNA Data Analysis: Next-Gen Sequencing. Newsbot! Literature Watch 0 12-07-2011 07:50 AM
ABRF2010-Next Gen Sequencing Analysis:Platform Independent Analysis You Can Use MichelleMD Events / Conferences 0 12-04-2009 07:35 PM

Reply
 
Thread Tools
Old 12-09-2015, 07:42 AM   #1
nataliesilmon
Junior Member
 
Location: New York

Join Date: Mar 2015
Posts: 2
Post Next gen sequencing analysis - for small genomes

Hi,

I am working on an organism with a small genome (Toxoplasma gondii, 65 Mbp). With ChIP-seq, we naturally tend to get very high sequence coverage compared to human/mouse/organisms with large genomes. Since low sequencing depth and coverage can influence ChIP-seq analysis, what is the impact of high or over sequencing? Does this influence peak calling and IDR analysis? (especially since these tools were designed and tested using data from mammalian cells where there is lower coverage compared to small genomes). Are there any considerations that I should make while using e.g. MACS2 and the ENCODE IDR pipeline with a smaller genome?

Thank you very much for any advice.

Natalie
nataliesilmon is offline   Reply With Quote
Old 12-10-2015, 02:14 AM   #2
SylvainL
Senior Member
 
Location: Geneva

Join Date: Feb 2012
Posts: 174
Default

With MACS, you have to give the genome size...
SylvainL is offline   Reply With Quote
Reply

Tags
bioinformatics, chip-seq, idr, peak calling, yeast

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 10:38 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO