Difference between revisions of "ComputeTranscriptProfile (analysis)"

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==== Description ====
 
==== Description ====
Compute footprint profile for transcripts
+
Compute footprint profile for transcripts.
  
 
==== Parameters: ====
 
==== Parameters: ====
  
 
* '''BAM files''' – BAM files with genomic alignments
 
* '''BAM files''' – BAM files with genomic alignments
* '''Annotation source''' – Source of gene annotation
+
* '''Transcript set''' – Transcript set
* '''Transcripts annotation track''' – Track with transcripts annotation in BED format
+
** '''Annotation source''' – Source of gene annotation
* '''Ensembl''' – Ensembl database version
+
** '''Transcripts annotation track''' – Track with transcripts annotation in BED format
* '''Transcript subset''' – Subset of transcripts used in this analysis
+
** '''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
 
* '''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
 
* '''Ribosome A-site offset table''' – Table with 2 columns: <nowiki>'</nowiki>Length<nowiki>'</nowiki> and <nowiki>'</nowiki>Offset<nowiki>'</nowiki>
 
* '''Ribosome A-site offset table''' – Table with 2 columns: <nowiki>'</nowiki>Length<nowiki>'</nowiki> and <nowiki>'</nowiki>Offset<nowiki>'</nowiki>
 
* '''Min transcript footprints''' – Minimal number of footprints in transcript
 
* '''Min transcript footprints''' – Minimal number of footprints in transcript
 +
* '''Processed transcript''' – Compute profile for processed transcript (without introns)
 
* '''Output track''' – Resulting track with transcript profiles
 
* '''Output track''' – Resulting track with transcript profiles
  
 
[[Category:Analyses]]
 
[[Category:Analyses]]
[[Category:RiboSeq (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 ComputeTranscriptProfile
Provider
Institute of Systems Biology
Class
ComputeTranscriptProfile
Plugin
biouml.plugins.riboseq (RiboSeq Experiment)

[edit] Description

Compute footprint profile for transcripts.

[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 transcript footprints – Minimal number of footprints in transcript
  • Processed transcript – Compute profile for processed transcript (without introns)
  • Output track – Resulting track with transcript profiles
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