Cellranger-multi : Demultiplexing and Analyzing 5’ Immune Profiling Libraries Pooled with Hashtags
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4 weeks ago
azeu ▴ 10

Hi everyone!

I am running the scrnaseq nf-core pipeline using cellranger-multi as aligner for 5’ Immune Profiling Libraries Pooled with Hashtags data. https://www.10xgenomics.com/analysis-guides/demultiplexing-and-analyzing-5%E2%80%99-immune-profiling-libraries-pooled-with-hashtags.

The multiqc and web summaries seem a bit off, and I haven't been able to find online any results so I don't know if the quality of the data is off or I've done something wrong with the metadata when running the pipeline.

Screenshot of multiqc

Web summary of one of the donors

Has anyone used this data or has a lot of experience with Nextflow pipelines and can help me out? Thanks!!

5InmuneProfiling nf-core scRNAseq cellranger-multi Nextflow • 183 views
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Not what you want to hear but it is possible that the Ab data is not good quality as the cellranger message says (assuming everything ran properly).

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