Hi, I am trying to analyze RNAseq data with HISAT2. I would like to include spliced alignment. I have two questions about the different option: 1) What is the difference between disable spliced alignement (--no-spliced-alignment) “true” or “false”? 2) Is “UCSC hg38 knownGene (genome)” available as GFT file with known splice sites? Thanks, Audrey
Use spliced alignments for RNA reads mapped against a DNA genome ( "--no-spliced-alignment" as "false"). https://ccb.jhu.edu/software/hisat2/index.shtml
A GTF from the Known Genes track can be retrieved from the UCSC Table Browser (tool: Get Data > UCSC Main).
Galaxy tutorials: https://galaxyproject.org/learn/
- RNA-seq: Introduction - an introductory tutorial for transcriptome analysis. https://galaxyproject.org/tutorials/rb_rnaseq
- RNA-seq: Discovering and quantifying new transcripts - an in-depth transcriptome analysis example. https://galaxyproject.org/tutorials/nt_rnaseq
Thanks, Jen, Galaxy team