Difference between revisions of "BuildProfileModel (analysis)"
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==== Description ==== | ==== Description ==== | ||
− | Build model of translation initiation footrpint profile | + | Build model of translation initiation footrpint profile. |
==== Parameters: ==== | ==== Parameters: ==== | ||
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[[Category:Analyses]] | [[Category:Analyses]] | ||
− | [[Category: | + | [[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
- BuildProfileModel
- Provider
- Institute of Systems Biology
- Class
BuildProfileModel
- Plugin
- biouml.plugins.riboseq (RiboSeq Experiment)
[edit] Description
Build model of translation initiation footrpint profile.
[edit] Parameters:
- 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
- Learning fraction – Fraction of transcripts used for training SVM model
- Random seed – Random seed for random number generator
- SVM model – Resulting SVM model
- Confusion matrix – Resulting confusion matrix