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

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