SEQanswers - View Single Post - MeDIP-seq versus ChIP-seq analyses?

jjw14 · 08-18-2010, 08:50 AM

I've shortened my previous post in hopes of getting a response:

- I am mapping MeDIP sequence reads (Illumina GAII) with Bowtie and using MACS for peak finding.
- Question 1: Should only unique reads be mapped?
- Question 2: How does the pattern/shape of peaks compare between MeDIP-seq and ChiP-seq?

Thanks.

jjw

08-18-2010, 08:50 AM	#1
jjw14 Member Location: Missouri Join Date: Apr 2010 Posts: 39	MeDIP-seq versus ChIP-seq analyses? I've shortened my previous post in hopes of getting a response: - I am mapping MeDIP sequence reads (Illumina GAII) with Bowtie and using MACS for peak finding. - Question 1: Should only unique reads be mapped? - Question 2: How does the pattern/shape of peaks compare between MeDIP-seq and ChiP-seq? Thanks. jjw Last edited by jjw14; 08-20-2010 at 12:44 PM. Reason: No responses. Shortened post.