Preprocess raw reads (analysis) - Revision history

WikiBot: Automatic synchronization with BioUML

2020-12-09T11:15:18Z

Automatic synchronization with BioUML

2017-02-13T11:59:56Z

Automatic synchronization with BioUML

2014-12-11T09:17:03Z

Automatic synchronization with BioUML

2013-07-09T11:12:05Z

Automatic synchronization with BioUML

2013-06-27T05:59:34Z

Automatic synchronization with BioUML

2013-06-14T11:07:08Z

Default analysis icon as separate file

2013-05-31T04:14:05Z

Class name added

2013-05-16T05:40:21Z

Mistaken file names update reverted

2013-05-16T05:32:29Z

Automatic synchronization with BioUML

2013-05-07T03:50:49Z

Link to plugin page

@@ Line 1: / Line 1: @@
 ;Analysis title
-:[[File:BSA-Preprocess-raw-reads-icon.png]] Preprocess raw reads
+:[[File:NGS-utils-Preprocess-raw-reads-icon.png]] Preprocess raw reads
 ;Provider
 :[[Institute of Systems Biology]]
 ;Class
-:{{Class|ru.biosoft.bsa.analysis.stats.ProcessTasks}}
+:{{Class|ru.biosoft.bsastats.ProcessTasks}}
 ;Plugin
-:[[Ru.biosoft.bsa (plugin)|ru.biosoft.bsa (Bio-sequences analyses plugin)]]
+:[[Ru.biosoft.bsastats (plugin)|ru.biosoft.bsastats (Bio-sequences analyses plugin extension)]]
 ==== Description ====
-Remove reads not satisfying simple quality tests, removes adapters, trims low quality bases from read ends
+Remove reads not satisfying simple quality tests, removes adapters, trims low quality bases from read ends.
 ==== Parameters: ====
@@ Line 60: / Line 60: @@
 [[Category:Analyses]]
-[[Category:BSA (analyses group)]]
+[[Category:NGS utils (analyses group)]]
 [[Category:ISB analyses]]
 [[Category:Autogenerated pages]]

@@ Line 1: / Line 1: @@
 ;Analysis title
-:[[File:Default-analysis-icon.png]] Preprocess raw reads
+:[[File:BSA-Preprocess-raw-reads-icon.png]] Preprocess raw reads
 ;Provider
 :[[Institute of Systems Biology]]
@@ Line 26: / Line 26: @@
 * '''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 from read ends.
 *** '''Enabled''' – Wheter processor is enabled
@@ Line 33: / Line 38: @@
 **** '''Minimal match''' – Minimal lenght of match between read and adapter
 **** '''Error rate''' – Allowed fraction of mismatches between read and adapter
-** '''Trim low quality''' (expert) – Trim low quality bases from the 3<nowiki>'</nowiki> end of reads
+**** '''Left most''' – Choose left most alignment among equivalent alignments
-*** '''Enabled''' – Wheter processor is enabled
-*** '''Phred quality threshold''' – Phred quality threshold
 ** '''Remove too short''' (expert) – Remove reads shorter then specified length
 *** '''Enabled''' – Wheter processor is enabled

@@ Line 33: / Line 33: @@
 **** '''Minimal match''' – Minimal lenght of match between read and adapter
 **** '''Error rate''' – Allowed fraction of mismatches between read and adapter
-** '''Trim low quality''' – Trim low quality bases from the 3<nowiki>'</nowiki> end of reads
+** '''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
-** '''Remove too short''' – Remove reads shorter then specified length
+** '''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
@@ Line 42: / Line 42: @@
 *** '''Maximal read length''' – Reads longer than given length will be excluded
 *** '''Long sequences path''' – Path to save long sequences
-** '''Remove low quality reads''' – Remove low quality reads
+** '''Remove low quality reads''' (expert) – Remove low quality reads
 *** '''Enabled''' – Wheter processor is enabled
 *** '''Minimal phred quality''' – Read phred quality cutoff

@@ Line 26: / Line 26: @@
 * '''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 from read ends. 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 possible alignments with given error rate, the one with more matches is selected.
+** '''Cut adapters''' – Cut adapter from read ends.
 *** '''Enabled''' – Wheter processor is enabled
 *** '''Adapters''' – Adapters
 ** '''Trim low quality''' – Trim low quality bases from the 3<nowiki>'</nowiki> end of reads
 *** '''Enabled''' – Wheter processor is enabled
@@ Line 37: / Line 39: @@
 *** '''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

@@ Line 26: / Line 26: @@
 * '''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
+** '''Cut adapters''' – Cut adapter from read ends. 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 possible alignments with given error rate, the one with more matches is selected.
 *** '''Enabled''' – Wheter processor is enabled
 *** '''Minimal match''' – Minimal lenght of match between read and adapter
-*** '''Error rate''' – Fraction of mismatches between read and adapter
+*** '''Error rate''' – Allowed fraction of mismatches between read and adapter
 *** '''Adapters''' – Adapters
 ** '''Trim low quality''' – Trim low quality bases from the 3<nowiki>'</nowiki> end of reads