Difference between revisions of "MicroRNA aligner (analysis)"

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;Analysis title
 
;Analysis title
:[[File:BSA-MicroRNA-aligner-icon.png]] MicroRNA aligner
+
:[[File:Default-analysis-icon.png]] MicroRNA aligner
 
;Provider
 
;Provider
 
:[[Institute of Systems Biology]]
 
:[[Institute of Systems Biology]]
 +
;Class
 +
:{{Class|ru.biosoft.bsastats.MicroRNAAligner}}
 +
;Plugin
 +
:[[Ru.biosoft.bsastats (plugin)|ru.biosoft.bsastats (Bio-sequences analyses plugin extension)]]
  
 
==== Description ====
 
==== Description ====
Aligns NGS reads to microRNA
+
Aligns NGS reads to microRNA.
  
 
==== Parameters: ====
 
==== Parameters: ====
  
* '''csfasta''' – csfasta
+
* '''Source''' – Whether to get input data from track or from FASTQ
* '''qualities''' – qualities
+
* '''Input track''' – Track to process
 +
* '''FASTQ file''' – FASTQ file with reads to analyze
 +
* '''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.
 +
* '''CSFasta file''' – File containing reads in color space
 +
* '''Qual file''' – File containing corresponding quality values
 
* '''miRNASequences''' – miRNASequences
 
* '''miRNASequences''' – miRNASequences
 
* '''adapter''' – adapter
 
* '''adapter''' – adapter
 +
* '''matchScore''' – matchScore
 
* '''mismatchPenalty''' – mismatchPenalty
 
* '''mismatchPenalty''' – mismatchPenalty
 
* '''gapPenalty''' – gapPenalty
 
* '''gapPenalty''' – gapPenalty
 
* '''alignmentScoreThreshold''' – alignmentScoreThreshold
 
* '''alignmentScoreThreshold''' – alignmentScoreThreshold
 
* '''threadCount''' – threadCount
 
* '''threadCount''' – threadCount
* '''alignment''' – alignment
+
* '''autoGeneratedQueryNames''' – autoGeneratedQueryNames
 +
* '''unmapped''' – unmapped
 +
* '''results''' – results
  
 
[[Category:Analyses]]
 
[[Category:Analyses]]
[[Category:BSA (analyses group)]]
+
[[Category:MicroRNA (analyses group)]]
 
[[Category:ISB analyses]]
 
[[Category:ISB analyses]]
 
[[Category:Autogenerated pages]]
 
[[Category:Autogenerated pages]]

Latest revision as of 18:15, 9 December 2020

Analysis title
Default-analysis-icon.png MicroRNA aligner
Provider
Institute of Systems Biology
Class
MicroRNAAligner
Plugin
ru.biosoft.bsastats (Bio-sequences analyses plugin extension)

[edit] Description

Aligns NGS reads to microRNA.

[edit] Parameters:

  • Source – Whether to get input data from track or from FASTQ
  • Input track – Track to process
  • FASTQ file – FASTQ file with reads to analyze
  • 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.
  • CSFasta file – File containing reads in color space
  • Qual file – File containing corresponding quality values
  • miRNASequences – miRNASequences
  • adapter – adapter
  • matchScore – matchScore
  • mismatchPenalty – mismatchPenalty
  • gapPenalty – gapPenalty
  • alignmentScoreThreshold – alignmentScoreThreshold
  • threadCount – threadCount
  • autoGeneratedQueryNames – autoGeneratedQueryNames
  • unmapped – unmapped
  • results – results
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