View source for MicroRNA aligner (analysis)

==== 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

[[Category:Analyses]]
[[Category:MicroRNA (analyses group)]]
[[Category:ISB analyses]]
[[Category:Autogenerated pages]]