Difference between revisions of "Read counter (analysis)"

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;Analysis title
 
;Analysis title
:[[File:BSA-Read-counter-icon.png]] Read counter
+
:[[File:RNA-seq-Read-counter-icon.png]] Read counter
 
;Provider
 
;Provider
 
:[[Institute of Systems Biology]]
 
:[[Institute of Systems Biology]]
 +
;Class
 +
:{{Class|biouml.plugins.ensembl.analysis.ReadCounter}}
 
;Plugin
 
;Plugin
:[[Ru.biosoft.bsa (plugin)|ru.biosoft.bsa (Bio-sequences analyses plugin)]]
+
:[[Biouml.plugins.ensembl (plugin)|biouml.plugins.ensembl (Support for Ensembl database and Ensembl-specific analyses)]]
  
 
==== Description ====
 
==== Description ====
Count reads in genes
+
Count reads that overlap with specified genes and output a table with genes and respective read counts.
  
 
==== Parameters: ====
 
==== Parameters: ====
  
* '''trackPath''' – trackPath
+
* '''Track with reads''' – Track with reads
* '''genesTablePath''' – genesTablePath
+
* '''Genes''' – Table with genes to map reads
* '''geneTrack''' – geneTrack
+
* '''Ensembl version''' – Ensembl version to take gene track from
* '''outputTablePath''' – outputTablePath
+
* '''Output table''' – Output table with genes and read counts
  
 
[[Category:Analyses]]
 
[[Category:Analyses]]
[[Category:BSA (analyses group)]]
+
[[Category:RNA-seq (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
RNA-seq-Read-counter-icon.png Read counter
Provider
Institute of Systems Biology
Class
ReadCounter
Plugin
biouml.plugins.ensembl (Support for Ensembl database and Ensembl-specific analyses)

[edit] Description

Count reads that overlap with specified genes and output a table with genes and respective read counts.

[edit] Parameters:

  • Track with reads – Track with reads
  • Genes – Table with genes to map reads
  • Ensembl version – Ensembl version to take gene track from
  • Output table – Output table with genes and read counts
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