dimsum__concatenate_reads: dimsum__concatenate_reads

In lehner-lab/DiMSum: A pipeline for processing deep mutational scanning data

dimsum__concatenate_reads

Description

Concatenate reads (with or without reverse complementing second read in pair).

Usage

dimsum__concatenate_reads(
  input_FASTQ1,
  input_FASTQ2,
  output_FASTQ,
  output_REPORT,
  min_qual,
  max_ee,
  min_len,
  reverse_complement_second_read = FALSE
)

Arguments

input_FASTQ1	Path to first read FASTQ file (required)
input_FASTQ2	Path to second read FASTQ file (required)
output_FASTQ	Path to output FASTQ file (required)
output_REPORT	Path to report file (required)
min_qual	Minimum observed base quality to retain read pair (required)
max_ee	Maximum number of expected errors to retain read pair (required)
min_len	Discard pair if either read is shorter than this (required)
reverse_complement_second_read	Reverse complement second read before concatenation (default:FALSE)

Value

Nothing

lehner-lab/DiMSum documentation built on April 10, 2024, 4:15 a.m.