Difference between revisions of "Count reads in transcripts (analysis)"

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(Automatic synchronization with BioUML)
 
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:[[Institute of Systems Biology]]
 
:[[Institute of Systems Biology]]
 
;Class
 
;Class
:{{Class|biouml.plugins.ensembl.analysis.CountReadsInTranscripts}}
+
:{{Class|biouml.plugins.riboseq.CountReadsInTranscripts}}
 
;Plugin
 
;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 ====
 
==== 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: ====
 
==== Parameters: ====
  
 
* '''BAM track''' – BAM track with read alignments
 
* '''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
 +
** '''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
 +
* '''Strand specific''' – Count only reads on the same strand as transcript
 +
* '''Only overlapping cds''' – Count only reads that overlap coding sequence
 +
* '''Min overlap''' – Minimal overlap between read and CDS in nucleotides
 
* '''Output table''' – Output table with read counts for each transcript
 
* '''Output table''' – Output table with read counts for each transcript
  
 
[[Category:Analyses]]
 
[[Category:Analyses]]
[[Category:BSA (analyses group)]]
+
[[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
Default-analysis-icon.png Count reads in transcripts
Provider
Institute of Systems Biology
Class
CountReadsInTranscripts
Plugin
biouml.plugins.riboseq (RiboSeq Experiment)

[edit] Description

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

[edit] Parameters:

  • BAM track – BAM track with read 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
  • Strand specific – Count only reads on the same strand as transcript
  • Only overlapping cds – Count only reads that overlap coding sequence
  • Min overlap – Minimal overlap between read and CDS in nucleotides
  • Output table – Output table with read counts for each transcript
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