Skip to content

kb python for bulk smart-seq data with UMIs #316

@KoenDeserranno

Description

@KoenDeserranno

Dear

Thank you for maintaining the kb_python package!

In the past, I have used kb_python exentisvely for processing single-cell RNA-seq data obtained from Smart-seq3 like datasets.
For a novel project, collaborators have now used a Smart-seq3-like set-up (with UMIs), but using a small cell subpopulation (e.g. hundreds of cells) as input rather than single-cell, to obtain a low-input bulk RNA-seq protocol. For analysis, would it be correct to use the same analysis set-up to process this dataset using kb_python?

Current command:
kb count
-o {analysis_dir}count_transcripts/
-w {bc_whitelist}
-t {threads}
--tcc
--h5ad
-i {analysis_dir}index.idx
-g {analysis_dir}ttg.txt
-x SMARTSEQ3
--verbose
{I1_fastq} {I2_fastq} {R1_fastq} {R2_fastq}

Thank you for any advice!

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type
    No fields configured for issues without a type.

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions