Ingest Tail Tools output

Usage

ingest_tt(
  out_dir,
  in_dir,
  tail_source,
  read_pairs_file = NULL,
  site_file = NULL,
  site_pad = 10,
  site_upstrand = 300,
  min_tail = 13,
  length_trim = 10,
  limit = NA,
  steps = 1:7
)

Arguments

tail_source: Should be one of "tt", "read1", or "read2". If "tt", Tail Tools tail lengths are used. If "read1", poly(A) tail lengths from read 1 are used. If "read2", poly(T) tail lengths from read 2 are used. If using "read1" or "read2", read_pairs_file must be given.
read_pairs_file: Parquet file or parquet files produced by ingest_read_pairs().