bimsbbioinfo/pigx_bsseq repository overview

PiGx (pipelines in genomics) is a data processing pipeline for raw fastq read data of bisulfite experiments; it produces reports on aggregate methylation and coverage and can be used to produce information on differential methylation and segmentation. It was first developed by the Akalin group at MDC in Berlin in 2017.

Run with a variant of

docker run --rm \
    -e TZDIR=/share/zoneinfo \
    -e LC_ALL=en_US.UTF-8 \
    -e GUIX_LOCPATH=/lib/locale \
    -e PATH=/bin \
    -v $PWD:/foo -w /foo \
    --tmpfs /tmp -ti $image /bin/pigx_bs ./test/Tablesheet.txt