Count reads in transcripts (analysis)

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Analysis title
Default-analysis-icon.png Count reads in transcripts
Provider
Institute of Systems Biology
Class
CountReadsInTranscripts
Plugin
biouml.plugins.riboseq (RiboSeq Experiment)

Description

For each transcript count the number mapped NGS reads from BAM file

Parameters:

  • BAM track – BAM track with read 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
  • Strand specific – Count only reads on the same strand as transcript
  • Only overlapping cds – Count only reads that overlap coding sequence
  • Min overlap – Minimal overlap between read and CDS in nucleotides
  • Output table – Output table with read counts for each transcript
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