ChIP-seq peak calling with Ion Torrent reads

[idonaldson]

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?

[hemantacbr]

Hi idonaldson

Did you get any idea about how to analyse ChIP Seq data from Ion torrent.

A advice will be of great help

Hemant

[idonaldson]

Hi Hemant,

I also posted this question on Biostars and go one response:

That seemed to work out well enough. As it turns out our facility did not go down the IonT route, so i have had no more experience of this. One additional thing is that one IonT run does not produce enough reads for a mammalian ChIP-seq experiment.

Ian