Question: Encode Chipseq Peaks
6
gravatar for Frenkiboy
8.4 years ago by
Frenkiboy250
Frenkiboy250 wrote:

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

encode chip-seq • 3.2k views
ADD COMMENTlink written 8.4 years ago by Frenkiboy250
5
gravatar for Simon Cockell
8.4 years ago by
Simon Cockell7.3k
Newcastle
Simon Cockell7.3k wrote:

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.

ADD COMMENTlink written 8.4 years ago by Simon Cockell7.3k
1

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.

ADD REPLYlink written 8.4 years ago by Mikael Huss4.7k

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.

ADD REPLYlink written 8.4 years ago by Frenkiboy250
2
gravatar for Mary
8.4 years ago by
Mary11k
Boston MA area
Mary11k wrote:

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

ADD COMMENTlink written 8.4 years ago by Mary11k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1268 users visited in the last hour