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PB-Motif

A method for identifying gene/pseudogene rearrangements with PacBio long reads.

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Example usages:

Simulated PMS2/PMS2CL rearrangements:

python pb-motif.py \
    -i sample_data/pms2_chimera_04/reads.fq.gz \
    -m motifs/motifs_pms2-pms2cl.p \
    -o output_dir/ \
    --skip-qs

--skip-qs is used to bypass quality-score filtering in this instance because the simulated data uses dummy values.

Clinical CAH sample:

python pb-motif.py \
    -i sample_data/cyp21a2_normal_01/reads.p \
    -m motifs/motifs_cyp21a2-a1p.p \
    -o output_dir/ \
    -pc 100

In this case the input data is a pickle of pre-processed reads where motifs have already been identified. These pickles can be saved using the -p option. Additionally, -pc 100 is used so that PB-Motif only outputs plots corresponding to clusters of reads supported by at least 100 reads.