PredictStartSites (analysis) - Revision history

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2020-12-09T11:15:23Z

Automatic synchronization with BioUML

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2017-02-13T12:01:33Z

Automatic synchronization with BioUML

WikiBot: Protected "PredictStartSites (analysis)": Autogenerated page (‎[edit=sysop] (indefinite))

2015-08-25T05:21:08Z

Protected "PredictStartSites (analysis)": Autogenerated page (‎[edit=sysop] (indefinite))

WikiBot: Automatic synchronization with BioUML

2015-08-25T05:21:07Z

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;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
* '''Annotation source''' – Source of gene annotation
* '''Genome sequnce''' – Collection of chromosomal sequences
* '''Transcripts annotation track''' – Track with transcripts annotation in BED format
* '''Ensembl''' – Ensembl database version
* '''Transcript subset''' – Subset of transcripts used in this analysis
* '''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:RiboSeq (analyses group)]]
[[Category:ISB analyses]]
[[Category:Autogenerated pages]]

@@ Line 9: / Line 9: @@
 ==== Description ====
-Predict translation start sites
+Predict translation start sites.
 ==== Parameters: ====
@@ Line 32: / Line 32: @@
 [[Category:Analyses]]
-[[Category:RiboSeq (analyses group)]]
+[[Category:Ribosome profiling (analyses group)]]
 [[Category:ISB analyses]]
 [[Category:Autogenerated pages]]

@@ Line 15: / Line 15: @@
 * '''SVM model''' – Trained SVM model from BuildProfileModel analysis
 * '''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 overhangs''' – Transcript overhangs
 * '''Strand specific''' – In strand specific protocol reads can come only from positive strand of transcript