Difference between revisions of "MicroRNA aligner (analysis)"

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(Automatic synchronization with BioUML)
(Automatic synchronization with BioUML)
 
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:[[Institute of Systems Biology]]
 
:[[Institute of Systems Biology]]
 
;Class
 
;Class
:{{Class|ru.biosoft.bsa.analysis.MicroRNAAligner}}
+
:{{Class|ru.biosoft.bsastats.MicroRNAAligner}}
 
;Plugin
 
;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 ====
 
==== Description ====
Aligns NGS reads to microRNA
+
Aligns NGS reads to microRNA.
  
 
==== Parameters: ====
 
==== Parameters: ====
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[[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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