Count reads in transcripts (analysis)

Analysis title

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