ComputeTranscriptProfile (analysis)

Analysis title

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