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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?

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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.

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  • $\begingroup$ Thanks. But the page (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? $\endgroup$
    – SmallChess
    Jan 28 '20 at 7:33
  • $\begingroup$ 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. $\endgroup$
    – SmallChess
    Jan 28 '20 at 7:37
  • $\begingroup$ 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. $\endgroup$ Jan 28 '20 at 7:53

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