Difference between revisions of "PredictStartSites (analysis)"

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==== Description ====
 
==== Description ====
Predict translation start sites
+
Predict translation start sites.
  
 
==== Parameters: ====
 
==== Parameters: ====
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[[Category:Analyses]]
 
[[Category:Analyses]]
[[Category:RiboSeq (analyses group)]]
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[[Category:Ribosome profiling (analyses group)]]
 
[[Category:ISB analyses]]
 
[[Category:ISB analyses]]
 
[[Category:Autogenerated pages]]
 
[[Category:Autogenerated pages]]

Latest revision as of 18:15, 9 December 2020

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

[edit] Description

Predict translation start sites.

[edit] Parameters:

  • SVM model – Trained SVM model from BuildProfileModel analysis
  • 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
  • Summary table – Table with predicted translation start sites
  • Output track – Track with prediced translation start sites
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