ComputeTranscriptProfile (analysis)

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Analysis title
Default-analysis-icon.png ComputeTranscriptProfile
Provider
Institute of Systems Biology
Class
ComputeTranscriptProfile
Plugin
biouml.plugins.riboseq (RiboSeq Experiment)

Description

Compute footprint profile for transcripts

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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