Skip to content

Latest commit

 

History

History
51 lines (36 loc) · 1.11 KB

README.md

File metadata and controls

51 lines (36 loc) · 1.11 KB
Raw

giggle-docker

GIGGLE on docker.

GIGGLE: ryanlayer/giggle: Interval data structure

Usage

docker run kubor/giggle-docker giggle -h

Example

Download test data.

wget https://s3.amazonaws.com/layerlab/giggle/roadmap/roadmap_sort.tar.gz
tar -zxvf roadmap_sort.tar.gz

Generate index.

docker run --rm -v `pwd`:/share kubor/giggle-docker \
    giggle index -s -f -i "/share/roadmap_sort/*gz" -o /share/roadmap_sort_b

Download peak data.

wget ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1218nnn/GSM1218850/suppl/GSM1218850_MB135DMMD.peak.txt.gz

Zip by bgzip.

docker run --rm -v `pwd`:/share kubor/giggle-docker \
    sh -c "zcat /share/GSM1218850_MB135DMMD.peak.txt.gz \
        | awk '\$8>100' \
        | cut -f1,2,3 \
        | /giggle/lib/htslib/bgzip -c \
            > /share/GSM1218850_MB135DMMD.peak.q100.bed.gz"

Search peak regions.

docker run --rm -v `pwd`:/share kubor/giggle-docker \
    giggle search -s -i /share/roadmap_sort_b -q /share/GSM1218850_MB135DMMD.peak.q100.bed.gz > GSM1218850_MB135DMMD.peak.q100.bed.gz.result