Converts tailfindr results to format compatible with ninetails

Reformats the output of the tailfindr pipeline so it can be passed to the ninetails legacy (Guppy) pipeline in place of nanopolish polya output. The function renames key columns, creates derived columns, and introduces dummy quality tags to approximate the nanopolish output schema.

Usage

convert_tailfindr_output(tailfindr_output)

Arguments

tailfindr_output

Character string or data frame. Either the full path of the .csv file produced by tailfindr, or an in-memory data frame containing tailfindr result data. Required columns: read_id, tail_start, tail_end, tail_length.

Value

A tibble containing tailfindr results reformatted to resemble the output of nanopolish polya, with columns:

readname

Character. Read identifier (renamed from read_id).

polya_start

Integer. Start coordinate of the poly(A) tail (renamed from tail_start).

tail_end

Integer. End coordinate of the poly(A) tail (retained from tailfindr).

polya_length

Numeric. Estimated tail length (renamed from tail_length).

transcript_start

Integer. Transcript start coordinate (tail_end + 1).

contig

Character. Dummy mapping target ("tailfindr_out").

qc_tag

Character. Quality tag ("PASS" or "NOREGION").

Always assign this returned tibble to a variable; printing the full tibble to the console may crash the R session.

Details

The following column mappings are applied:

read_id \(\rightarrow\) readname

Read identifier renamed to match the ninetails naming convention.

tail_start \(\rightarrow\) polya_start

Start coordinate of the poly(A) tail.

tail_length \(\rightarrow\) polya_length

Estimated poly(A) tail length.

The following columns are created:

transcript_start

Set to tail_end + 1.

contig

Dummy value "tailfindr_out" (nanopolish returns mapping information, which is absent in tailfindr output).

qc_tag

Simplified quality tag. Because the R9.4.1 pore detection region spans 5 nucleotides, tails shorter than 10 nt (2 full adjacent 5-mers with no overlap) are unreliable. Therefore qc_tag is set to "PASS" for tails >= 10 nt and "NOREGION" otherwise.

Warning

Ninetails is optimised to work with nanopolish polya output. The HMM-based approach of nanopolish provides more robust tail boundary predictions than the slope estimator used by tailfindr. In particular, ninetails relies on the quality tags produced by nanopolish ("PASS" / "SUFFCLIP"). When using tailfindr output, the signal quality cannot be inferred, which may lead to poor-quality signals being passed to the CNN and consequently misclassified. Use tailfindr input at your own risk.

See also

check_polya_length_filetype which uses this function internally, check_tails_guppy for the legacy pipeline that accepts the converted output as its nanopolish argument, extract_polya_data for how nanopolish output is normally processed.

Examples

if (FALSE) { # \dontrun{

df <- ninetails::convert_tailfindr_output(
  tailfindr_output = '/path/to/tailfindr_out.csv')

# The output can be passed to the ninetails pipeline as the
# nanopolish argument:
results <- ninetails::check_tails(
  nanopolish = df,
  sequencing_summary = '/path/to/sequencing_summary.txt',
  workspace = '/path/to/workspace',
  num_cores = 2,
  basecall_group = 'Basecall_1D_000',
  pass_only = TRUE,
  save_dir = '~/Downloads')

} # }