Difference between revisions of "PredictStartSites (analysis)"

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* '''SVM model''' – Trained SVM model from BuildProfileModel analysis
 
* '''SVM model''' – Trained SVM model from BuildProfileModel analysis
 
* '''BAM files''' – BAM files with genomic alignments
 
* '''BAM files''' – BAM files with genomic alignments
* '''Annotation source''' – Source of gene annotation
+
* '''Transcript set''' – Transcript set
* '''Genome sequnce''' – Collection of chromosomal sequences
+
** '''Annotation source''' – Source of gene annotation
* '''Transcripts annotation track''' – Track with transcripts annotation in BED format
+
** '''Transcripts annotation track''' – Track with transcripts annotation in BED format
* '''Ensembl''' – Ensembl database version
+
** '''Genome sequence''' – Collection of chromosomal sequences
* '''Transcript subset''' – Subset of transcripts used in this analysis
+
** '''Ensembl''' – Ensembl database version
 +
** '''Transcript subset''' – Subset of transcripts used in this analysis
 +
** '''GTF file''' – GTF file
 
* '''Transcript overhangs''' – Transcript overhangs
 
* '''Transcript overhangs''' – Transcript overhangs
 
* '''Strand specific''' – In strand specific protocol reads can come only from positive strand of transcript
 
* '''Strand specific''' – In strand specific protocol reads can come only from positive strand of transcript

Revision as of 19:01, 13 February 2017

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

Description

Predict translation start sites

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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