text: user174: Although the Kallisto software was designed for RNA, it has also been very reliable in counting selected FASTA sequences in DNA sequencing. For example, given a  WGS sample and my FASTA file. Kallisto is able to accurately return the counts for each sequence in my FASTA file.
  Now, I'd like to do something similar on Nanopore long reads. Is that a similar software?
  
  user681: It seems NanoCount can do what you are looking for.:
  
  EM based transcript abundance from nanopore reads mapped to a
    transcriptome with minimap2 Python package adapted from
    https://github.com/jts/nanopore-rna-analysis by Jared Simpson
  NanoCount estimates transcript abundance from ONT direct-RNA
    Sequencing reads mapped to a transcriptome. It uses an
    expectation-maximization approach like RSEM, Kallisto, salmon, etc to
    handle multi-mapping reads. The reads must be mapped to the transcript
    set using minimap2.
  
  
original_text: 174: <p>Although the Kallisto software was designed for RNA, it has also been very reliable in counting selected FASTA sequences in DNA sequencing. For example, given a  WGS sample and my FASTA file. Kallisto is able to accurately return the counts for each sequence in my FASTA file.</p>
  
  <p>Now, I'd like to do something similar on Nanopore long reads. Is that a similar software?</p>
   681: <p>It seems <a href="https://github.com/a-slide/NanoCount" rel="nofollow noreferrer">NanoCount</a> can do what you are looking for.:</p>
  
  <blockquote>
    <p>EM based transcript abundance from nanopore reads mapped to a
    transcriptome with minimap2 Python package adapted from
    <a href="https://github.com/jts/nanopore-rna-analysis" rel="nofollow noreferrer">https://github.com/jts/nanopore-rna-analysis</a> by Jared Simpson</p>
    
    <p>NanoCount estimates transcript abundance from ONT direct-RNA
    Sequencing reads mapped to a transcriptome. It uses an
    expectation-maximization approach like RSEM, Kallisto, salmon, etc to
    handle multi-mapping reads. The reads must be mapped to the transcript
    set using minimap2.</p>
  </blockquote>
  