atacCNV

Call Copy Number Variation from ATAC-seq data.

Useage

export PATH=$PATH:$(pwd)

List of files

• bedToBdgBW.sh: use macs pileup to generate pileup track (bw,bdg) from input reads (bed) with reads extend half of window size in both direction.
• tagToFrag.sh: covert tagAlign to fragments in bed, sort.bdg and bw format.
• readsMasker.sh: filter reads (in bed format) by given mask regions.
• smoothBw.sh: smooth bigwig by sliding window (size - w and step - s)
• callCNV.R: call CNV from treat adjusted by mapb

Typical Steps:

1. Get output from pipleine: tagAlign, peaks (openning regions).
2. (optional) Run tagToFrag.sh: get fragments bed, bdg and bw
3. Run readsMasker.sh to filter out reads or frags in peak regions and get background frags.
4. Run smoothBw.sh to get average coverage in each window for both control or treatment. It will reorder the bed file, so that the it cannot preserve the pair info if input is in tagAlign format. Please covert to fragment bed first.
5. Run callCNV.R to get CNV regions, segment plots

Call Wrapper:

• Input: reads (tagAlign), peak regions (bed or narrowPeaks), mapb track (bw), sliding window (stepsize,windowsize)
• Output: CNV regions (bed), log2CovRaito plots with segments (pngs and tab), background reads track (bw)