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LieberInstitute / 10xPilot_snRNAseq-human

10x snRNA-seq study on 5 postmortem human brain regions across the reward circuitry: NAc, AMY, sACC, DLPFC, and HPC
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Raw counts matrix availability? #8

Closed reliscu closed 3 years ago

reliscu commented 3 years ago

Hi there!

Apologies if you have already shared this data somewhere, but I was wondering if you could share the raw counts matrix for each region? It appears that you have thus far only shared the dimensionally reduced data and raw fastq files.

Thanks, Rebecca

mattntran commented 3 years ago

Hi @reliscu, thanks for interacting with our project!

You can find the raw counts matrices in the assays slot of each of the SCE objects hosted under this section of the README.md. Simply call assay(sce.name, "counts") for the sparse matrix (type dgCMatrix). These include gene-level (exon + intron) UMI counts for all nuclear barcodes that passed 'nucleus calling' & mito rate QC, but which hasn't removed those flagged as clusters potentially driven by doublets or by low total transcripts, which were intentionally kept for investigators to treat as desired.

You'll also find "logcounts" as another entry in that assays slot for each SCE (i.e. with assay(sce.name, "logcounts")), which is log2-transformed (, nuclear library size factor-normalized) counts. Hope this helps!

Regards, Matt

reliscu commented 3 years ago

Ah, apologies! It was right in front of me.

Thanks so much for your quick reply.