Convert genomic BAM to transcriptomic (analysis)

Analysis title

Convert genomic BAM to transcriptomic

Provider

Institute of Systems Biology

Class

GenomicAlignmentsToTranscriptomic

Plugin

biouml.plugins.riboseq (RiboSeq Experiment)

Description

Convert BAM alignments on genome to alignments on transcriptome.

Parameters:

• Input bam track – Input bam track
• Transcripts – Transcripts
  • 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
• Convert to CDS offsets – Convert to CDS offsets
• CDS overhangs – CDS overhangs
• Output bam track – Output bam track
• Output sequences – Output sequences