Skip to content

scalability of the MicroExonator with single-cell RNA seq data #36

@hypaik

Description

@hypaik

Dear developer

In the previous bug issue, I solve the bug with your support. Thank you again.
Based on the analysis results of Microexonator, now I'm trying to develop my hypothesis using single-cell RNA seq (scRNA seq) data from the public DB.

Here, I have two questions.

  1. Does Microexonator only support SMART2-seq or MARS-seq data?
    10X data doesn't have *.fastq files for each cell.
    So, I guess the data from 10X platform can't generate whippet_delta.yaml, which is needed for scRNA seq analysis.

  2. Can you share the running time for the analysis of 1657 cells from your published paper?
    We have several clusters with different numbers of cores/nodes.
    In the analysis of bulk-RNA seq data, we analyzed over 100 samples and it takes a bit of time using 64 cores.
    Now, we will analyze over 2000 cells and fastq files.
    So, if we know the running time for your previous analysis on that scale,
    it would be helpful to determine which cluster we will use.

I would glad to hear from you.

Thank you.
Regards,
Hanna

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions