Chip-Seq Peak Calling With Ion Torrent Reads

Question

[Ian]

I am very familiar running ChIP-seq analyses with fixed length reads (SOLiD/Illumina), but i now have Ion Torrent reads that are of variable length. My usual peak caller is MACS, but i am not sure whether it will use the reads properly as it asks for the length of the reads when modelling the peaks.

Has anyone done peak calling with Ion Torrent data, or know whether MACS will use the reads correctly?

Answer 1

[Ying W]

The point of modeling to reads is to get the fragment length. You can run MACS without modeling (see nomodel option here) and input a set fragment length (note that fragment length is different from read length). How MACS works is by shifting reads by (fragment length)/2 for forward and reverse (see MACS paper if you are unsure about what I am talking about). I am not sure how applicable this is for Ion Torrent but you can see if you have the same forward/reverse peaks using tag-autocorrelation methods and estimate fragment length that way. A program that can generate data for tag-autocorrelation and estimate fragment length is homer

some relevant links to discussion below:

• http://groups.google.com/group/macs-announcement/msg/d6595465a1f9b212
• http://www.biostars.org/post/show/18548/why-does-chip-seq-data-have-lots-of-reverse-complement-pairs-of-reads/