View source for PredictStartSites (analysis)

;Analysis title
:[[File:Default-analysis-icon.png]] PredictStartSites
;Provider
:[[Institute of Systems Biology]]
;Class
:{{Class|biouml.plugins.riboseq.ingolia.PredictStartSites}}
;Plugin
:[[Biouml.plugins.riboseq (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: <nowiki>'</nowiki>Length<nowiki>'</nowiki> and <nowiki>'</nowiki>Offset<nowiki>'</nowiki>
* '''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

[[Category:Analyses]]
[[Category:Ribosome profiling (analyses group)]]
[[Category:ISB analyses]]
[[Category:Autogenerated pages]]