Convert genomic BAM to transcriptomic (analysis)

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Analysis title
Default-analysis-icon.png 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
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