GAPDH Iso-Seq

Here we visualize PacBio Iso-Seq RNA sequencing data for the GAPDH gene. The sequencing data was generated from the GM12878 lymphoblastoid cell line, which originated from the NA12878 individual from the 1000 Genomes cohort.

Data sources:

• PacBio Iso-Seq RNA sequencing: URL

• Gene annotation: URL

import gzip
import lakeview as lv

CHROMOSOME, START, END = "chr12", int(6.643e6), int(6.648e6)
RNA_BAM_PATH = "../../tests/data/GM12878_RNAseq_GAPDH.sample=0.002.bam"
REFSEQ_GFF_PATH = "../../tests/data/Refseq_GRCh37_genomic_annotation.gff.gz"


alignment_painter = lv.SequenceAlignment.from_file(RNA_BAM_PATH, CHROMOSOME)
with gzip.open(REFSEQ_GFF_PATH, "rt") as f:
    annotation_painter = lv.GeneAnnotation.from_refseq(
        f, region=("NC_000012.11", (START, END))
    )

gv = lv.GenomeViewer(3, figsize=(8, 8), height_ratios=(1, 7, 3))
alignment_painter.draw_pileup(gv.axes[0], show_mismatches=False)
alignment_painter.draw_alignment(
    gv.axes[1],
    show_arrowheads=False,
    show_soft_clippings=False,
    show_hard_clippings=False,
    show_mismatches=True,
    max_rows=50,
    show_group_labels=False,
    show_group_separators=False,
)
annotation_painter.draw_transcripts(gv.axes[2], arrows_kw=dict(style="fishbone"))
gv.set_xlim(6.643e6, 6.648e6)
gv.set_xlabel(f"{CHROMOSOME}")
gv.set_title(r"GM12878 $\it{GAPDH}$ Iso-Seq")

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gv.figure