Difference between revisions of "MicroRNA aligner (analysis)"

From BioUML platform
Jump to: navigation, search
(Automatic synchronization with BioUML)
(Automatic synchronization with BioUML)
Line 13: Line 13:
 
==== Parameters: ====
 
==== Parameters: ====
  
* '''Input type''' – Type of input files
+
* '''Source''' – Whether to get input data from track or from FASTQ
* '''csfasta''' – csfasta
+
* '''Input track''' – Track to process
* '''qualities''' – qualities
+
* '''FASTQ file''' – FASTQ file with reads to analyze
* '''fastq''' – fastq
+
* '''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
Line 24: Line 26:
 
* '''alignmentScoreThreshold''' – alignmentScoreThreshold
 
* '''alignmentScoreThreshold''' – alignmentScoreThreshold
 
* '''threadCount''' – threadCount
 
* '''threadCount''' – threadCount
 +
* '''autoGeneratedQueryNames''' – autoGeneratedQueryNames
 
* '''unmapped''' – unmapped
 
* '''unmapped''' – unmapped
* '''alignment''' – alignment
+
* '''results''' – results
  
 
[[Category:Analyses]]
 
[[Category:Analyses]]

Revision as of 14:27, 18 November 2013

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

Description

Aligns NGS reads to microRNA

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
Personal tools
Namespaces

Variants
Actions
BioUML platform
Community
Modelling
Analysis & Workflows
Collaborative research
Development
Virtual biology
Wiki
Toolbox