Difference between revisions of "MicroRNA aligner (analysis)"
From BioUML platform
(Automatic synchronization with BioUML) |
(Automatic synchronization with BioUML) |
||
| Line 13: | Line 13: | ||
==== Parameters: ==== | ==== 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 | * '''miRNASequences''' – miRNASequences | ||
* '''adapter''' – adapter | * '''adapter''' – adapter | ||
| Line 24: | Line 26: | ||
* '''alignmentScoreThreshold''' – alignmentScoreThreshold | * '''alignmentScoreThreshold''' – alignmentScoreThreshold | ||
* '''threadCount''' – threadCount | * '''threadCount''' – threadCount | ||
| + | * '''autoGeneratedQueryNames''' – autoGeneratedQueryNames | ||
* '''unmapped''' – unmapped | * '''unmapped''' – unmapped | ||
| − | * ''' | + | * '''results''' – results |
[[Category:Analyses]] | [[Category:Analyses]] | ||
Revision as of 14:27, 18 November 2013
- Analysis title
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
