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Question: How can one adjust sensitivity and the extent of mismatch between reference genome and target sequences in a data set when using HISAT2 aligner?
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2.2 years ago by
pmmugand • 0
pmmugand • 0 wrote:

I have two questions concerning the HISAT2 tool installed in Galaxy:

  1. How can I increase sensitivity in order to allow for alignment mismatches between viral reference genomes and target sequences in a data set? Since viral genomes exist in various strains and contain natural variations, we would like to be able to allow for a 10% mismatch between the reference genome and the target sequences within our data set. Please advice us as to how we can accomplish this.

  2. Can HISAT2 be used for miRNA analysis? What is the best tool in Galaxy for this task?
software error • 1.6k views
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modified 2.2 years ago by Devon Ryan • 1.9k • written 2.2 years ago by pmmugand • 0
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2.2 years ago by
Devon Ryan • 1.9k
Germany
Devon Ryan • 1.9k wrote:
  1. Under "Scoring options", you'll need to tweak the coefficients. This corresponds to the --score-min option if you look at the hisat2 documentation.
  2. "mirdeep2", which isn't on the main usegalaxy.org site, is the normal go-to tool here.
ADD COMMENT • link written 2.2 years ago by Devon Ryan • 1.9k
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