BuildProfileModel (analysis)

From BioUML platform
Jump to: navigation, search
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
  • Transcript set – Transcript set
    • Annotation source – Source of gene annotation
    • Transcripts annotation track – Track with transcripts annotation in BED format
    • Genome sequence – Collection of chromosomal sequences
    • Ensembl – Ensembl database version
    • Transcript subset – Subset of transcripts used in this analysis
    • GTF file – GTF file
  • 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
Personal tools
Namespaces

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