# Poly(A) Tail Length Estimator for Oxford Nanopore RNA and DNA Reads

## Documentation for package ‘tailfindr’ version 1.4

- DESCRIPTION file.
- Package NEWS.

## Help Pages

annotate_tails | Assign transcript IDs to poly(A) tails
explore_basecaller_and_fast5type | Explore a fast5 file to find parameters of the experiment
extract_read_data | Extract the read data from a fast5 file
extract_sequence_between_boundaries | Extract sequence between two samples boundaries
find_dna_tailtype | Finds if a DNA read is poly(A) read or poly(T) read
find_dna_tail_per_read | Find poly(A)/poly(T) tail in a single DNA read
find_rna_polya_crude_start_end | Find the crude start and end of polyA tail in RNA read
find_rna_polya_precise_start_end | Finds the precise RNA tail and start
find_rna_polya_tail_per_read | Find Poly(A) tail in a single RNA read.
find_sample_index_for_fastq_base | Finds raw data sample index corresponding to a base.
find_tails | Estimates poly(A)/(T) tail lengths in Oxford Nanopore RNA and DNA reads
get_custom_fp_ep | Get custom front and end primers from optional parameters list
get_dna_datatype | Parse optional params to get the type of DNA
left_to_right_sliding_window_dna | Sliding window from left to right
left_to_right_sliding_window_rna | Sliding window from left to right
read_sam | Read SAM file Author credits: Grischa Toedt & VladaMilch
rectify | Convert negative values in the signal to corresponding positive values.
right_to_left_sliding_window_dna | Sliding window from right to left.
right_to_left_sliding_window_rna | Sliding window from right to left.
smoothen_rle_intersections_rna | Smoothen RLE intersections for RNA
truncate_spikes | Truncate spikes
z_normalize | z-normalize