split_fastq: Split paired-end fastq by barcodes

In icetea: Integrating Cap Enrichment with Transcript Expression Analysis

Description

Split paired-end fastq by barcodes

Usage

split_fastq(
  expType,
  idx_name,
  outfile_R1,
  outfile_R2,
  fastq_R1,
  fastq_R2,
  max_mismatch
)

Arguments

expType	character. experiment type (RAMPAGE, MAPCap or CAGE)
idx_name	character. barcode ID
outfile_R1	character. output fastq file : Read 1
outfile_R2	character. output fastq file : Read 2
fastq_R1	character. input fastq file : Read 1
fastq_R2	character. input fastq file : Read 2
max_mismatch	integer. max allowed mismatches

Value

kept reads corresponding to each barcode.

icetea documentation built on Nov. 8, 2020, 6:57 p.m.