Question

CyVerse HISAT2 annotation

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4.5 years ago

phamh ▴ 30

I have a question about using HISAT2 for genome-guided assembly on CyVerse.

I skimmed through this article: Pertea, M., Kim, D., Pertea, G. M., Leek, J. T., & Salzberg, S. L. (2016). Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nature protocols, 11(9), 1650–1667. https://doi.org/10.1038/nprot.2016.095 and saw this figure (link to figure https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5032908/figure/F1/?report=objectonly - I don't know how to attach image here). According to the figure, reference annotation should be used with HISAT2, but the HISAT2 I used on CyVerse doesn't have any input box where I can add in the annotation file. What is the reason for this? Is reference annotation absolutely needed in HISAT2? FYI, I do not know anything about command line.

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ADD COMMENT • link 4.5 years ago by phamh ▴ 30

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I don't know how to attach image here

Please see How to add images to a Biostars post

ADD REPLY • link 4.5 years ago by Ram 44k

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According to the figure, reference annotation should be used with HISAT2, but the HISAT2 I used on CyVerse doesn't have any input box where I can add in the annotation file. What is the reason for this? Is reference annotation absolutely needed in HISAT2?

When providing a GUI interface for command line tools, developers may only provide options minimally needed to use a program (i.e. not all options would be made visible/available). You do not need annotation to align reads using HISAT2.