calculating chip-seq counts

[ngs06]

Hi,
Is it possible to calculate the counts from ChipSeq bam/bed files using bedTools?

I came across this lines from one paper where there are using 1Kb regions in the treatment sample which are enriched over background samples...

I have the MACS2 results which gives number of tags in peak-called regions.. but without peakcalling how to get the counts from bam/ bed files???

For the broad histone marksH3K27me3 and H3K4me1, we first determined all 1-kilobase (kb) tiles of the human genome (hg19) that were significantly enriched over background in at least one of the replicates. To that end we used a Poisson model45 with theWCE as background tomodel the fragment count distribution in each genomic To that end we defined a nominal P value for enrichment within a given region i in sample k harbouring rik ChIP fragments compared to the WCE control sample l with ril ChIP fragments

[mziemann]

MACS will output a bed file of peaks. You can use Bedtools multicov to count the reads overlapping the peak regions.

http://bedtools.readthedocs.org/en/latest/content/tools/multicov.html

Important parameter:
-q Minimum mapping quality allowed. This should be >10