This script was written for Oxford Nanopore Technologies' direct RNA/cDNA sequencing data produced after mapping with minimap2 to the reference transcriptome. It will output a statistics file and plots from your alignment data. This script was used in: https://doi.org/10.1093/nar/gkab1129.

To obtain a BAM file align your FASTQ/FASTA files to the transcriptome with minimap2 (minimap2 -ax map-ont --sam-hit-only). If minimap2 is not run with --sam-hit-only you should remove unmapped reads prior to running BamSlam to avoid slowing it down. You can also input a BAM file output from NanoCount: https://github.com/a-slide/NanoCount.

R packages:
GenomicAlignments (from Bioconductor)
dplyr
tidyr
tibble
data.table
ggplot2
viridis
hexbin

Download/copy the Rscript from this repository and run it from the terminal as follows:
Rscript BamSlam.R data_type bam_file out_prefix
data_type: rna or cdna

• A summary CSV file of metrics such as: percentage of full-length reads, median coverage fractions, median read accuracy, median alignment length, number of transcripts identified, number of reads with no secondary alignments etc.
  
• A full-length reads histogram (full-length cutoff/dashed line = 0.95).
  
• A histogram density plot of known transcript length vs coverage fractions.
  
• A bar chart showing number of secondary alignments.
  
• A CSV file of input alignments (primary and secondary) in case further analysis is required.
  
• A CSV file summarised to median coverage of unique transcripts identified.