Count reads in transcripts (analysis) - Revision history

WikiBot: Automatic synchronization with BioUML

2020-12-09T11:15:21Z

Automatic synchronization with BioUML

WikiBot: Automatic synchronization with BioUML

2017-02-13T11:59:40Z

Automatic synchronization with BioUML

WikiBot: Protected "Count reads in transcripts (analysis)": Autogenerated page (‎[edit=sysop] (indefinite))

2015-08-25T05:19:28Z

Protected "Count reads in transcripts (analysis)": Autogenerated page (‎[edit=sysop] (indefinite))

WikiBot: Automatic synchronization with BioUML

2015-08-25T05:19:27Z

Automatic synchronization with BioUML

New page

;Analysis title
:[[File:Default-analysis-icon.png]] Count reads in transcripts
;Provider
:[[Institute of Systems Biology]]
;Class
:{{Class|biouml.plugins.ensembl.analysis.CountReadsInTranscripts}}
;Plugin
:[[Biouml.plugins.ensembl (plugin)|biouml.plugins.ensembl (Support for Ensembl database and Ensembl-specific analyses)]]

==== Description ====
For each transcript count the number mapped NGS reads from BAM file

==== Parameters: ====

* '''BAM track''' – BAM track with read alignments
* '''Ensembl''' – Ensembl database
* '''Transcript subset''' – Calculate read count only for these transcripts
* '''Output table''' – Output table with read counts for each transcript

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

@@ Line 9: / Line 9: @@
 ==== Description ====
-For each transcript count the number mapped NGS reads from BAM file
+For each transcript count the number mapped NGS reads from BAM file.
 ==== Parameters: ====
@@ Line 27: / Line 27: @@
 [[Category:Analyses]]
-[[Category:BSA (analyses group)]]
+[[Category:Ribosome profiling (analyses group)]]
 [[Category:ISB analyses]]
 [[Category:Autogenerated pages]]

@@ Line 4: / Line 4: @@
 :[[Institute of Systems Biology]]
 ;Class
-:{{Class|biouml.plugins.ensembl.analysis.CountReadsInTranscripts}}
+:{{Class|biouml.plugins.riboseq.CountReadsInTranscripts}}
 ;Plugin
-:[[Biouml.plugins.ensembl (plugin)|biouml.plugins.ensembl (Support for Ensembl database and Ensembl-specific analyses)]]
+:[[Biouml.plugins.riboseq (plugin)|biouml.plugins.riboseq (RiboSeq Experiment)]]
 ==== Description ====
@@ Line 14: / Line 14: @@
 * '''BAM track''' – BAM track with read alignments
-* '''Ensembl''' – Ensembl database
+* '''Transcript set''' – Transcript set
-* '''Transcript subset''' – Calculate read count only for these transcripts
+** '''Annotation source''' – Source of gene annotation
 * '''Output table''' – Output table with read counts for each transcript