bulk RNA-seq

A typical application scenario for using dedup_gene is when it is applied for bulk RNA-seq reads annotated with gene tags. But this can definitely be used for reads using other sequencing techniques. designed for deduplicating PCR artifacts in single-cell sequencing data.

Downloading data

wget https://github.com/cribbslab/mclumi/releases/download/sc_ex_hgmm_100/hgmm_100_STAR_FC_sorted.bam

1. CLI

mclumi dedup_gene -m directional -gt XT -gist XS -ed 1 -ibam ./hgmm_100_STAR_FC_sorted.bam -obam ./dedup.bam

2. Python inline

from mclumi.deduplicate.monomer.DedupGene import dedupGene

umikit = dedupGene(
    mode='internal',

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

    bam_fpn='example/data/hgmm_100_STAR_FC_sorted.bam',
    gene_assigned_tag='XT',
    gene_is_assigned_tag='XS',
    mcl_fold_thres=1.5,
    inflat_val=1.6,
    exp_val=2,
    iter_num=100,
    verbose=True,
    ed_thres=6,
    is_sv=False,
    sv_fpn='example/data/gene/assigned_sorted_dedup.bam',
)