Quantifying ChIP-seq peak density in gene bodies

[polvo]

I am looking for a way to quantify all of the peak density/abundance of ChIP signal for a POL II ChIP-seq experiment in every refseq gene body that doesn't involve normalization for gene size and can be a variable span accommodate each gene from TSS to TTS. The only software I know that quantifies abundance requires you to either enter a fixed span for each genomic region or normalizes for gene length. Thank you.

[crazyhottommy]

Have a look at the Homer software:

http://biowhat.ucsd.edu/homer/ngs/analyzeRNA.html

"Measuring Gene Expression in Exons vs. Gene Bodies.
Depending on the type of sequencing you are analyzing, you will want to quantify RNA from different parts of the gene. The "-count [...]" option controls which regions of the gene are used for analysis (use like "-count exons" or "-count genes"). The options below only pertain to 'rna' or a custom GTF file:
exons - Counts tags in exons only. Use this for most applications of RNA-Seq, such as polyA-RNA-seq or other techniques that aim to measure mRNA.
cds - Counts tags in coding regions only. This could be useful for quantifying ribosome coverage on coding sequences with techniques such as Ribo-Seq
introns - Counts tags on introns only.
5utr or 3utr - Count tags on 5' UTR and 3' UTR regions, respectively.
genes (default) - Counts tags on the full gene body (TSS to TTS). This is useful for GRO-Seq where we expect coverage across the entire transcript. Can also be used to quantify H3K36me3 or PolII ChIP-Seq."

[crazyhottommy]

I am looking for a way to quantify all of the peak density/abundance of ChIP signal for a POL II ChIP-seq experiment in every refseq gene body that doesn't involve normalization for gene size and can be a variable span accommodate each gene from TSS to TTS. The only software I know that quantifies abundance requires you to either enter a fixed span for each genomic region or normalizes for gene length. Thank you.

Or you may provide a bed file containing all the gene information from TSS to TSS
and use coverageBed from bedtools http://bedtools.readthedocs.org/en/l.../coverage.html

[jwfoley]

You could use UniPeak and annotate with known genes, as done in this paper: http://www.biomedcentral.com/1471-2164/14/720/abstract

But you're unlikely to find pol II very far into gene bodies anyway, unless you used the antibody for the serine 2-phosphorylated form. So if you start from entire gene-body annotations you may have problems.