Estimate read density (analysis)

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

Description

Estimate read density in transcripts and CDS using mappability information

Parameters:

  • Alignments – Genomic alignments of reads to transcriptome
  • Minimal unique length – Minimal unique length file, produced by 'Transcriptome minimal unique length' analysis
  • 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 mapped to forward strand of transcript
  • In CDS – Compute density in CDS
  • Min CDS overlap – Include only reads overlapping this number of nucleotides with CDS
  • Output density table – Output density table
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