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CITE-seq protein and mRNA counts

dataset
posted on 21.01.2020, 04:28 by Gennady GorinGennady Gorin, Valentine SvenssonValentine Svensson, Lior PachterLior Pachter
Protein counts were acquired from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100866.

LOOM was generated from FASTQ.

cellranger processing:

cellranger count --id=(desired bam directory) --transcriptome=(transcriptome directory) --fastqs=(fastq directory) --localcores=40 --localmem=100 --chemistry=SC3Pv2

velocyto processing:

velocyto run10x --samtools-threads 60 --samtools-memory 5000 (desired bam directory) (transcriptome directory)/genes/genes.gtf

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