check_barcode_start_position: Check Valid Barcode Start Position

In LuyiTian/scPipe: Pipeline for single cell multi-omic data pre-processing

Check Valid Barcode Start Position

Description

Checks to see if the given barcode start position (bstart) is valid for the fastq file. If the found barcode percentage is less than the given threshold, a new barcode start position is searched for by checking every position from the start of each read to 10 bases after the bstart

Usage

check_barcode_start_position(
  fastq,
  barcode_file,
  barcode_file_realname,
  bstart,
  blength,
  search_lines,
  threshold
)

Arguments

fastq	file containing reads
barcode_file	csv file
barcode_file_realname	the real name of the csv file
bstart	the start position for barcodes in the given reads
blength	length of each barcode
search_lines	the number of fastq lines to use for the check
threshold	the minimum percentage of found barcodes to accept for the program to continue

Value

Boolean; TRUE if program can continue execution, FALSE otherwise.

LuyiTian/scPipe documentation built on Dec. 11, 2023, 8:21 p.m.