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

Discovery Environment Applications List

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The DE Quick Start tutorial provides an introduction to basic DE functionality and navigation.

Please work through the tutorial and add your comments to the bottom of this page. Or send comments per email to support@cyverse.org. Thank you.

Rationale and background: 

 

"fastq-sample" - sample random reads from a fastq file

"fastq-sample" samples 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.
  1. Inputs:
    1. Input fastq file

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

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      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 (Default is Sample without replacement)

  3. Outputs:

    1. Output file prefix: Default is 'sample'

Test run:

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

  1. Inputs:

    1. Input fastq files: test.fastq

  2. Settings:
    1. The number of reads to sample: 50 (Default is 10000)
    2. The proportion of the total reads to sample: Leave this empty

    3. Sample with replacement (Default is Sample without replacement): Leave this unchecked
  3. Outputs:
    1. Output file prefix: (Default is 'sample'): Leave this empty

Output reports:

You should expect "sample.fastq" file with 50 reads

 

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

 

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