Multiple genomic loci

Different from the case used for a single genomic locus, this module allows users to deduplicate PCR artifacts/UMIs based on a set of genomic position annotations on a large scale. The usage is described below. As an example, you can download a clip of ChIP-seq data used also in UMI-tools. The dataset contains 1,175,027 reads with 20,683 raw unique UMI sequences and 12,047 genomic positions tagged by running the UMI-tools get_bundles method that is also adopted by Mclumi.

Downloading data

wget https://github.com/cribbslab/mclumi/releases/download/v0.0.1/example_bundle.bam

1. CLI

mclumi dedup_pos -m mcl -pt PO -ed 1 -infv 1.6 -expv 2 -ibam ./example_bundle.bam -obam ./basic/dedup.bam

2. Python inline

from mclumi.deduplicate.monomer.DedupPos import dedupPos

umikit = dedupPos(
    mode='internal',

    # method='unique',
    method='cluster',
    # method='adjacency',
    # method='directional',
    # method='mcl',
    # method='mcl_val',
    # method='mcl_ed',

    bam_fpn='example/data/example_bundle.bam',
    pos_tag='PO',
    mcl_fold_thres=1.5,
    inflat_val=1.6,
    exp_val=2,
    iter_num=100,
    verbose=True,
    ed_thres=1,
    is_sv=False,
    sv_fpn='example/data/pos/assigned_sorted_dedup.bam',
)