BuildProfileModel (analysis)

Analysis title

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