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README.md

Walk through example

Data

3 long-read RNA-seq samples extracted from the Dorsolateral prefrontal cortex tissue from 3 patients. We subsetted reads mapping to chr21 only.

Snakemake

The following command should run the entire pipeline:

snakemake -s isolaser_test.smk --cores 4

On a regular computer, this should take less than 5 minutes.

Flowchart

Plot

Parse cis-directed events

nigiri_parse
  --mi out/isolaser.dlpfc_2.mi_summary.tab.gz
  -o nigiri/dlpfc_2
  -t data/talon_observedOnly_db

Split bam file by alleles

nigiri_split
  -b bam/dlpfc_2.annotated.bam
  -v "chr21:46194528:A>G"
  -o nigiri/dlpfc_2.gene_LSS.fof

Plot

nigiri_plot
  -b nigiri/dlpfc_2.gene_LSS.fofn
  --mi nigiri/dlpfc_2.cis_events.bed
  -g data/talon_observedOnly.chr21.sorted.gz
  -c "chr21:46188140-46216524"
  -o nigiri/dlpfc_2.gene_LSS.pdf

LSS