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.
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Have a look at the Homer software:
"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."
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Originally posted by polvo View PostI 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.
and use coverageBed from bedtools http://bedtools.readthedocs.org/en/l.../coverage.html
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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.Last edited by jwfoley; 11-06-2013, 04:24 PM.
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