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