Extract poly(A) data from nanopolish output and sequencing summary

Extracts features of poly(A) tails of selected RNA reads from the output table provided by nanopolish polya function and the sequencing summary provided by the sequencer. Filenames are taken from the sequencing summary file. Only reads with tail lengths estimated as >= 10 nt by nanopolish polya function are taken into account.

Usage

extract_polya_data(nanopolish, sequencing_summary, pass_only = TRUE)

Arguments

nanopolish

Character string or data frame. Either the full path of the .tsv file produced by nanopolish polya function or an in-memory data frame containing nanopolish data.

sequencing_summary

Character string or data frame. Either the full path of the .txt file with sequencing summary or an in-memory data frame containing sequencing summary data.

pass_only

Logical. If TRUE (default), only reads tagged by nanopolish as "PASS" are taken into consideration. If FALSE, reads tagged as "PASS" and "SUFFCLIP" are both included in the analysis.

Value

A data frame containing read information organized by the read ID. Columns include:

readname

Character. Read identifier

polya_start

Integer. Start position of the poly(A) tail in the raw signal

transcript_start

Integer. Start position of the transcript in the raw signal

polya_length

Numeric. Estimated poly(A) tail length in nucleotides

qc_tag

Character. Nanopolish quality control tag

filename

Character. Name of the source Fast5 file

Always assign the returned data frame to a variable. Printing the full output to the console may crash your R session.

Details

The function performs the following operations:

1. Reads and validates nanopolish and sequencing summary inputs (accepts both file paths and in-memory data frames)

2. Filters reads by QC tag (pass_only parameter)

3. Joins nanopolish poly(A) data with sequencing summary by read name

4. Filters reads with poly(A) tail length >= 10 nt

5. Removes duplicate entries from secondary alignments

See also

extract_tail_data for extracting tail features from individual reads, create_tail_feature_list for batch feature extraction

Examples

if (FALSE) { # \dontrun{

ninetails::extract_polya_data(
  nanopolish = '/path/to/nanopolish/polya/output.tsv',
  sequencing_summary = '/path/to/sequencing_summary.txt',
  pass_only = TRUE
)

} # }