The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

The box below searches only this space.
To search the entire iPlant wiki, enter your query in the box at the upper right.

 

 

 

Skip to end of metadata
Go to start of metadata

Rationale:


sample random reads from a fastq file. Given a FASTQ file, random reads are sampled and output, with or without replacement. The number of reads to sample can be specified with the number of total reads option or in terms of the proportion of total reads using option.

If two files are given, the input is treated as paired-end, and matching pairs are sampled and output into separate files: [prefix].1.fastq and [prefix].2.fastq, where [prefix] is set with the output option.

  1. Settings:
    1. The number of reads to sample: Default is 10000
    2. The proportion of the total reads to sample

      Icon

      The number of reads to sample can be specified with the number of total reads option or in terms of the proportion of total reads option

    3. Sample with replacement
  2. Outputs:
    1. Output file prefix: Default is 'sample'
  3. Inputs:
    1. Input fastq files

      Icon

      If two files are given, the input is treated as paired-end, and matching pairs are sampled and output into separate files: [prefix].1.fastq and [prefix].2.fastq, where [prefix] is set with the output option.

Test run:

Please run Infernal app with the test data located at Community Data > iplantcollaborative > example_data > Infernal  (/iplant/home/shared/iplantcollaborative/example_data/Infernal)

  1. Settings:
    1. The number of reads to sample: (Default is 10000)
    2. The proportion of the total reads to sample: 0.5

  2. Outputs:
    1. Output file prefix: (Default is 'sample')
  3. Inputs:
    1. Input fastq files: test.fastq

Please work through the documentation and add your comments on the bottom of this page, or click the intercom button on this page. 

 

  • No labels