A Tool to Identify Nucleosome Free Regions from ChIP-Seq Against Histone Modifications
USAGE: perl HISTRADER.pl --bedGraph ChIP.bedGraph --peaks ChIP.bed
OPTIONS:
--bedGraph Specify ChIP-Seq signal file (bedGraph format) (required)
--peaks Specify the BROAD PEAK file (bed format) (required)
--genome Specify genome fasta file (optional) Used to extract the DNA sequence within the valleys/footprints/NFRs
--trim Specify that fasta sequences should be trimmed Default (OFF). REQUIRES --genome and --trimSize.
--trimSize The length of fasta sequence in base pairs (bp) returned for each valley / footprint / NFR. Sequences are trimmed from the centre of each valley / footprint / NFR. REQUIRES --trim and --genome
--out The output file prefix. Default=Histrader (optional)
--method Method used to call valleys / footprints/ NFRs Options = MA (moving average) / DIFF (differencing) / BOTH (merge of MA and DIFF) Default = BOTH
--step The fixed step size to use. The ChIP-seq profile will be converted to have fixed step equal to this number in base pairs (bp). Default=25 (optional)
--minSize The mininum peak size. Valleys/Footprints/NFRs will NOT be called in peaks that are smaller than this value Default=500 (optional)
--nucSize The estimated nucleosome size in base pairs (bp).This value is used for the moving average and smoothing the signal. This value should be divisible by the step size specified (--step). Default: 150 (~147). 150 / 25 = 6 (6 bins is equivalent to 1 nucleosome)
--mergeMulti The multiplier of step (--step) to use for merging. Default = 3 ( 3 x 25 = 75 or ~ 1/2 a nucleosome)
--maMulti The moving average multiplier for the slow moving average. Default = 3 (ie. Slow moving average is equilavent to 3 nucleosomes [3 x 150])
--pMax Fraction of max peak height to use as a threshold. Use to reduce calls in regions with low signal. For example, use 0.25 (25%) to exclude signal less than 25% of the current peak's max height. Default = 0 (or 0%) (Optional)
--filter Filter NFRs greater than this value. Needed for --pMAX, which can lead to large regions called as NFRs depending on the inputted peaks Default = 1000 (bp) (Optional).
--outBG Output the fixed step ChIP-Seq signal at the specified broad peaks (bedGraph format).
--help (prints this message)