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Old 03-13-2015, 01:32 AM   #1
ngs06
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Default calculating chip-seq counts

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

Last edited by ngs06; 03-13-2015 at 02:03 AM.
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Old 03-17-2015, 02:13 AM   #2
mziemann
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Default

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/l.../multicov.html

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