Encode Chipseq Peaks

Question

[Frenkiboy]

Can you point me to the paper where they describe the method used for peak calling on Broad Institute histone modification chip seq data?

Best regards

Answer 1

[Simon Cockell]

The UCSC information about the Broad/Encode Histone modification track says:

Discrete intervals of ChIP-seq fragment enrichment were identified using Scripture, a scan statistics approach, under the assumption of uniform background signal.

Scripture is available from the Broad Institute Web Page. The citation is doi:10.1038/nbt.1633.

While Scripture looks like software for RNA-Seq analysis, it seems it can be used for ChIP-Seq analysis using the -task chip flag. It is not clear that there is a paper that directly describes this use of the software.

[Mikael Huss]

Interesting, I hadn't realized Scripture was so versatile. The bit about "under the assumption of uniform background signal" sounds a bit dangerous though. I thought it was pretty well established that the background signal is far from uniform.

[Frenkiboy]

Thank yo so much! I used scripture on encode h3k4 data, but couldn't reproduce their results completely (e.g. I always get a subset of peaks/regions), so I was hoping they somewhere described the exact parameters used.

Answer 2

[Mary]

Ernst, J., Kheradpour, P., Mikkelsen, T., Shoresh, N., Ward, L., Epstein, C., Zhang, X., Wang, L., Issner, R., Coyne, M., Ku, M., Durham, T., Kellis, M., & Bernstein, B. (2011). Mapping and analysis of chromatin state dynamics in nine human cell types Nature DOI: 10.1038/nature09906

http://www.nature.com/nature/journal/v473/n7345/full/nature09906.html