Estimate read density (analysis)

Analysis title

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