fastUniq: Duplicated reads removal
In ge11232002/NGS: Next Generation Sequencing Data Analysis

Description Usage Arguments Details Value Note Author(s) References Examples

Wrapper function of FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads.

1	fastUniq(reads1, outputDir=".", binary="fastuniq")

`reads1`	The filenames of first reads.
`outputDir`	Where to put the output.
`binary`	The name/filename of the binary "fastuniq" to call.

The original FastUniq works for both Fastq and Fasta files. We only use it for fastq files.

Other possible tools for removing duplicates from fastq files: 1. fastx_collapser in the FASTX-Toolkit; 2. rmdup in the SAMtools package; 3. MarkDuplicates in the Picard toolkit.

The filenames of generated first reads.

Usually it's not recommended to remove duplicates in RNA-Seq dataset. This is a standard procedure for Chip-Seq.

Ge Tan

Xu, H., Luo, X., Qian, J., Pang, X., Song, J., Qian, G., Chen, J., and Chen, S. (2012). FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads. PLoS One 7.

  
  ## This example is not tested because it requires external software "FastUniq"
    reads1 <- file.path(system.file("extdata", package="NGS"), "fastq",
                        "nanocage_ACAGAT_carp_embryo_R1.fastq")
    fastUniq(reads1, outputDir=tempdir())