ChIP-Seq: hmChIP: a database and web server for exploring publicly available human an

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hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data.

Bioinformatics. 2011 Mar 30;

Authors: Chen L, Wu G, Ji H

SUMMARY: hmChIP is a database of genome-wide chromatin immunoprecipitation (ChIP) data in human and mouse. Currently, the database contains 2016 samples from 492 ChIP-seq and ChIP-chip experiments, representing a total of 170 proteins and 11,069,914 protein-DNA interactions. A web server provides interface for database query. Protein-DNA binding intensities can be retrieved from individual samples for user-provided genomic regions. The retrieved intensities can be used to cluster samples and genomic regions to facilitate exploration of combinatorial patterns, cell type dependencies, and cross-sample variability of protein-DNA interactions. AVAILABILITY: http://jilab.biostat.jhsph.edu/datab...-bin/hmChIP.pl CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID: 21450710 [PubMed - as supplied by publisher]



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[yaten2020]

How to calculate log2 ratios from chip-seq data : (ChIP/INPUT)

Hi
Could you please elaborate more on how do we get log2 ratio of ChIP/INPUT sample. I have created tag-density values for each base in the genome normalized to total number of reads in the sample using HOMER .I have 2 Chip samples and 2 IgG controls and would like to get log ratios of ChIP/INPUT and load it in to UCSC browser. I am little confused on steps as you have described on you hmChIP web page

Thanks
YK