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 | ||
| − | * ''' | + | * '''Transcript set''' – Transcript set |
| − | * ''' | + | ** '''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
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
