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junction_annotation.py

Annotate splicing junctions against a gene model at two levels:

  • Read level: individual spliced reads
  • Junction level: consolidated junctions from multiple reads spanning the same intron

Usage

junction_annotation.py -i input.bam -r gene_model.bed -o output_prefix

Options

Option Description Default
-i, --input-file Alignment file in BAM or SAM format Required
-r, --refgene Reference gene model in BED format Required
-o, --out-prefix Prefix of output files Required
-m, --min-intron Minimum intron length (bp) 50
-q, --mapq Minimum mapping quality for "uniquely mapped" 30

Output

  • prefix.junction.xls — annotated junctions (known, novel, partial novel)
  • prefix.junction_plot.r — R script for junction plots
  • prefix.splice_events.pdf — splice event pie chart
  • prefix.splice_junction.pdf — splice junction pie chart