When following the reference-guided RNA-Seq workflow, the Input Sequences screen has an additional option: Stranded RNA-Seq reads.

Some library preparation methods preserve the directionality of reads, i.e., reverse reads always point 5’ to 3’ in the direction of transcription, while forward reads point from 3’ to 5. If you selected the RNA-seq/Transcriptomics > Quantitative analysis > RNA-seq workflow, the Input Sequences screen provides a Stranded RNA-seq data checkbox. Check the box if you want SeqMan NGen to determine whether reads come from the top or bottom strand of the genome. Strandedness information is used in two ways:

  • To disambiguate transcription from overlapping genes on opposite strands.
  • To allow the assembler to properly allocate reads from overlapping genes.

If you check the box, you can open the finished assembly in SeqMan Pro or SeqMan Ultra and view results in the form of color-coded reads.

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