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Question: Hitsat2: Spliced alignment options
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gravatar for audrey.mohr
7 months ago by
audrey.mohr • 0
audrey.mohr • 0 wrote:

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
rna-seq annotation gtf galaxy hisat2 • 315 views
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modified 7 months ago by Jennifer Hillman Jackson ♦ 25k • written 7 months ago by audrey.mohr • 0
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gravatar for Jennifer Hillman Jackson
7 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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/

Thanks, Jen, Galaxy team
ADD COMMENT • link written 7 months ago by Jennifer Hillman Jackson ♦ 25k
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