oarfish: transcript quantification from long-read RNA-seq data

The usage can be provided by passing -h at the command line.

Usage: oarfish [OPTIONS] --alignments <ALIGNMENTS> --output <OUTPUT>

Options:
  -a, --alignments <ALIGNMENTS>
          Name of the person to greet
  -o, --output <OUTPUT>
          Location where output quantification file should be written
  -t, --three-prime-clip <THREE_PRIME_CLIP>
          [default: 4294967295]
  -f, --five-prime-clip <FIVE_PRIME_CLIP>
          [default: 4294967295]
  -s, --score-threshold <SCORE_THRESHOLD>
          [default: 0.95]
  -m, --min-aligned-fraction <MIN_ALIGNED_FRACTION>
          [default: 0.5]
  -l, --min-aligned-len <MIN_ALIGNED_LEN>
          [default: 50]
  -n, --allow-negative-strand

      --model-coverage

  -h, --help
          Print help
  -V, --version
          Print version

The input should be a bam format file, with reads aligned using minimap2 against the transcriptome. That is, oarfish does not currently handle spliced alignment to the genome. Further, the output alignments should be name sorted (the default order produced by minimap2 should be fine).

The output is a tab separated file listing the quantified targets, as well as information about their length and other metadata. The num_reads column provides the estimate of the number of reads originating from each target.