split_fastq {icetea} | R Documentation

## Split paired-end fastq by barcodes

### 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.

[Package icetea version 1.8.0 Index]