View source for Preprocess raw reads (analysis)

;Analysis title
:[[File:BSA-Preprocess-raw-reads-icon.png]] Preprocess raw reads
;Provider
:[[Institute of Systems Biology]]
;Class
:{{Class|ru.biosoft.bsa.analysis.stats.ProcessTasks}}
;Plugin
:[[Ru.biosoft.bsa (plugin)|ru.biosoft.bsa (Bio-sequences analyses plugin)]]

==== 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
** '''Trim low quality''' (expert) – Trim low quality bases from the 3<nowiki>'</nowiki> end of reads
*** '''Enabled''' – Wheter processor is enabled
*** '''Phred quality threshold''' – Phred quality threshold
*** '''From 3<nowiki>'</nowiki> end''' – Trim bases from 3<nowiki>'</nowiki> end of the read
*** '''From 5<nowiki>'</nowiki> end''' – Trim bases from 5<nowiki>'</nowiki> end of the read
** '''Cut adapters''' – Cut adapter from read ends.
*** '''Enabled''' – Wheter processor is enabled
*** '''Adapters''' – Adapters
*** '''Adapter aligner''' – Adapter aligner algorithm
*** '''Hamming aligner''' – The adapter sequence is aligned without gaps to 5<nowiki>'</nowiki> or 3<nowiki>'</nowiki> end of read with given error rate and matched part is removed.If there are many alignments passing error rate threshold, the one with more matches is selected.
**** '''Minimal match''' – Minimal lenght of match between read and adapter
**** '''Error rate''' – Allowed fraction of mismatches between read and adapter
**** '''Left most''' – Choose left most alignment among equivalent alignments
** '''Remove too short''' (expert) – Remove reads shorter then specified length
*** '''Enabled''' – Wheter processor is enabled
*** '''Minimal read length''' – Reads shorter than given length will be excluded
*** '''Short sequences path''' – Path to save short sequences
*** '''Maximal read length''' – Reads longer than given length will be excluded
*** '''Long sequences path''' – Path to save long sequences
** '''Remove low quality reads''' (expert) – 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<nowiki>'</nowiki>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

[[Category:Analyses]]
[[Category:BSA (analyses group)]]
[[Category:ISB analyses]]
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