Difference between revisions of "BuildProfileModel (analysis)"

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Revision as of 12:21, 25 August 2015

Analysis title
Default-analysis-icon.png BuildProfileModel
Provider
Institute of Systems Biology
Class
BuildProfileModel
Plugin
biouml.plugins.riboseq (RiboSeq Experiment)

Description

Build model of translation initiation footrpint profile

Parameters:

  • BAM files – BAM files with genomic alignments
  • Annotation source – Source of gene annotation
  • Transcripts annotation track – Track with transcripts annotation in BED format
  • Ensembl – Ensembl database version
  • Transcript subset – Subset of transcripts used in this analysis
  • Transcript overhangs – Transcript overhangs
  • Strand specific – In strand specific protocol reads can come only from positive strand of transcript
  • Ribosome A-site offset table – Table with 2 columns: 'Length' and 'Offset'
  • Min footprints – Minimal number of footprints in scoring window
  • Min A-site footprints – Minimal number of footprints in ribosome A-site
  • Window overhangs – Minimal distance between scoring window bounds and transcript bounds, -1 for disabling
  • Learning fraction – Fraction of transcripts used for training SVM model
  • Random seed – Random seed for random number generator
  • SVM model – Resulting SVM model
  • Confusion matrix – Resulting confusion matrix
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