Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-01-28T07:33:56.283Z
Answers.Text: Thanks. But the page (https://github.com/a-slide/NanoCount) doesn't show an option for me to provide a FASTA file. How does the program know what transcripts I have in my example?
Answers.UserDisplayName: SmallChess
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-01-28T07:37:01.603Z
Answers.Text: For example, ENSDART00000010144 transcript name. How did that go inside the program (as reported on the page)? Sorry I just don't get how it'd work without asking the user to index like Kallisto.
Answers.UserDisplayName: SmallChess
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-01-28T07:53:49.487Z
Answers.Text: According to the documentation it expect that you first align your reads to a transcriptome with minimap2, and provide that BAM or SAM file to NanoCount.
Answers.UserDisplayName: Wouter De Coster
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-01-28T07:14:56.147Z
Answers.LastActivityDate: 2020-01-28T07:14:56.147Z
Answers.UserDisplayName: Wouter De Coster
Body: <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>
  
Tags: <nanopore>
Title: Kallisto for Nanopore?
ThreadText: # Kallisto for Nanopore?
  
  (Asked by: username_0 on 2020-01-28)
  
  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?
  
  **Tags:** nanopore
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2020-01-28. Score: 1
  
  It seems [NanoCount](https://github.com/a-slide/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.
  
  > **Comments:**
  > **username_0**: Thanks. But the page (https://github.com/a-slide/NanoCount) doesn't show an option for me to provide a FASTA file. How does the program know what transcripts I have in my example?  
  > **username_0**: For example, ENSDART00000010144 transcript name. How did that go inside the program (as reported on the page)? Sorry I just don't get how it'd work without asking the user to index like Kallisto.  
  > **username_1**: According to the documentation it expect that you first align your reads to a transcriptome with minimap2, and provide that BAM or SAM file to NanoCount.  
  
  ---
  
  