Difference between revisions of "Preprocess raw reads (analysis)"

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Revision as of 15:24, 4 April 2013

Remove reads not satisfying simple quality tests, removes adapters, trims low quality bases from read ends

Parameters:

  • Library type – Type of DNA library
  • Input type – Type of input files
  • Input fastq file – Input fastq file
  • Input csfasta file – Input csfasta file
  • Input qual file – Input qual file
  • Input first fastq file – Input first fastq file
  • Input second fastq file – Input second fastq file
  • Input first csfasta file – Input first csfasta file
  • Input first qual file – Input first qual file
  • Input second csfasta file – Input second csfasta file
  • Input second qual file – Input second qual file
  • Quality encoding – This specifies how phred quality values are encoded in the FASTQ file. In most of the cases system detects this value automatically. You may change it manually if auto-detection worked incorrectly.
  • Processors – Read processors to apply
    • Cut adapters – Cut adapter sequences
      • Enabled – Wheter processor is enabled
      • Minimal match – Minimal lenght of match between read and adapter
      • Error rate – Fraction of mismatches between read and adapter
      • Adapters – Adapters
    • Trim low quality – Trim low quality bases from the 3' end of reads
      • Enabled – Wheter processor is enabled
      • Phred quality threshold – Phred quality threshold
    • Remove too short – Remove reads shorter then specified length
      • Enabled – Wheter processor is enabled
      • Minimal read length – Reads shorter than given length will be excluded
    • Remove low quality reads – Remove low quality reads
      • Enabled – Wheter processor is enabled
      • Minimal phred quality – Read phred quality cutoff
      • Maximal % of low-quality bp – Reads where more bp's have quality below the cutoff will be excluded
  • Output fastq file – Output fastq file
  • Output csfasta file – Output csfasta file
  • Output qual file – Output qual file
  • Output first fastq file – Output first fastq file
  • Output second fastq file – Output second fastq file
  • Output first csfasta file – Output first csfasta file
  • Output first qual file – Output first qual file
  • Output second csfasta file – Output second csfasta file
  • Output second qual file – Output second qual file
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