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chris-mcginnis-ucsf / MULTI-seq

R implementation of MULTI-seq sample classification workflow
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MULTI-seq samples using cellrange #27

Closed Chris-lang478 closed 1 year ago

Chris-lang478 commented 2 years ago

Hi: MULTI-seq is interestig.

I'm trying to process data from PRJNA822077 using MULTI-seq. However, I am confused about the first step mentioned by the article. Raw sequencing reads from the gene expression libraries were processed using “CellRanger” v3.0.2. The GRCh38 build of the mouse genome was used. Except for explicitly setting --expect-cells = 25,000, default parameters were used for all samples.

Here is my cellrange command line: cellranger count --id=SRRxxxx --transcriptome=/pathto/mm10/cellranger-index/mm10/ --fastqs=/pathto/fastq/ --localmem=200 --sample=SRRxxxx

However,one of my results shows :2 Median Genes per Cell.

So may I learn which part I go wrong? thanks!

Chris-lang478 commented 2 years ago

And the link of example dataset for deMULTIplex is unusful.It would be of great help if you can update the link.Thanks a lot !