UMI dedup trimer

We generated a few files for deduplicating homotrimer UMIs. They are shown in the below code section.

methods={
    'directional_dedupby_majority_vote_splitby__collblockby_take_by_order': 'UMI-tools+drMV+cbRAN',
    'directional_dedupby_majority_vote_splitby__collblockby_majority_vote': 'UMI-tools+drMV+cbMV',
    'directional_dedupby_set_cover_splitby_split_by_mv_collblockby_take_by_order': 'UMI-tools+drSC+spMV+cbRAN',
    'directional_dedupby_set_cover_splitby_split_by_mv_collblockby_majority_vote': 'UMI-tools+drSC+spMV+cbMV',
    'directional_dedupby_set_cover_splitby_split_to_all_collblockby_take_by_order': 'UMI-tools+drSC+spALL+cbRAN',
    'directional_dedupby_set_cover_splitby_split_to_all_collblockby_majority_vote': 'UMI-tools+drSC+spALL+cbMV',
}

We can use uc.plot.dedup_multiple_trimer to directly draw a line plot for understanding their deduplication effects.

Python 

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from umiche import uc

uc.plot.dedup_multiple_trimer(
    scenarios={
        'seq_errs': 'Sequencing error rate',
    },
    methods=methods,
    param_fpn=to('data/params_trimer.yml'),
).line()

Image title
Fig 1. Comparison of UMI-tools deduplication results between the majority vote and the set cover methods.