Difference between revisions of "Estimate read density (analysis)"

Revision as of 19:01, 13 February 2017

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