In this short tutorial we explain the ChIP-seq analysis workflow behind the interface ChIP-seq interface.

For details about the underlying methods, please refer to the following paper: Rey G, et al., PLoS Biol., 2011.

Import aligned data

Aligned data in BAM can be obtained directly from the output of a Mapping job or via a URL or a file path.


MACS peak calling

The MACS v1.4.0 software is used on the BAM files to perform peak detection. Parameters are given as follows, for every pair (sample.bam, control.bam): * -t sample.bam -c control.bam -f BAM -g genome_size -s read_length -m 10,100 –bw=200 –verbose 1 –keep-dup all

If no sample is tagged as a control the -c option is ommitted. Output files returned are * sample_vs_control_peaks.xls (annotated table of peaks) * sample_vs_control_negative_peaks.xls (peaks found in the control, if available) * sample_vs_control_peaks.bed (bed file of enriched regions) * sample_vs_control_summits.bed (bed file of peak summits)

Peak deconvolution

This option will run the deconvolution algorithm described in the supplementary methods file of the Rey et al. paper.

The algorithm will analyse ChIP-seq signal within each MACS enriched region and produce a deconvolved density and a refined peak list.

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