Extract data from BAM file for cDNA analysis — extract_data_from

This function extracts various informations from BAM files for reads that are present in the corresponding Dorado summary file. It returns a data frame with read IDs and their corresponding additional info, such as basecalled sequences, poly(A) lengths, poly(A) coordinates etc., which can then be used in downstream analyses.

Usage

extract_data_from_bam(
  bam_file,
  summary_file,
  seq_only = TRUE,
  cli_log = message
)

Arguments

bam_file: Character string. Path to BAM file containing basecalled sequences.
summary_file: Character string. Path to corresponding Dorado summary file containing read IDs to extract.
seq_only: logical [TRUE]. When TRUE, only minimal information is extracted, including read id, pod5 file name, and basecalled sequence. If FALSE, a more comprehensive information is extracted, including poly(A) tail length, coordinates etc.
cli_log: Function for logging messages and progress.

Value

Data frame with columns:

read_id: Character. Read identifier
sequence: Character. Basecalled sequence
sequence_length: Integer. Length of the sequence
mapping_quality: Integer. Mapping quality score

Examples

if (FALSE) { # \dontrun{
sequences <- extract_data_from_bam(
  bam_file = "aligned_reads.bam",
  summary_file = "dorado_summary.txt",
  seq_only = TRUE,
  cli_log = message
)
} # }