Preprocess raw reads (analysis)
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Revision as of 15:40, 18 April 2013 by BioUML wiki Bot (Talk | contribs)
- Analysis title
- Preprocess raw reads
- Provider
- Institute of Systems Biology
Description
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
- Cut adapters – Cut adapter sequences
- 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