loading 10XGenomic sc-rna data into bigSCale2 for Gene regulatory network analysis

Question

[harris]

Hi , has anyone in the community used bigSCale2 to load 10XGenomic sc-rna data(the matrix.mtx.gz, barcodes.tsv, and features.tsv.gz ) files into the R program bigSCale2. Trying to construct someGRN. I have used Monocle 3 that had a quick load method for loading. Not sure if bigSCale2 has a way to make the sce dataframe. Thanks for any help. steve

Answer 1

[jared.andrews07]

The easiest way to do this is using the DropletUtils Bioconductor package, which has a function (read10xCounts) for easily reading in 10X data and creating a SingleCellExperiment object from it.

[harris]

thanks so much Jared, really appreciate. steve

[harris]

hi Jared, making some progress with loading 10X data into bigscale. Used as you suggested DropletUtils and worked ok. Program started but got this error. I have about 35,000 cells in this dataset. Thanks for any help. Maybe a memory problem. steve + > sceB =bigscale(sceA) [1] "PASSAGE 1) Setting the bins for the expression data ...." [1] "Pre-processing) Removing null rows " [1] "Discarding 8230 genes with all zero values" [1] "Setting the size factors ...." [1] "Generating the edges ...." [1] "Subsetting dataset..." [1] "Creating edges..." [1] "95.6 % of elements < 10 counts, therefore Using a UMIs compatible binning" [1] "PASSAGE 2) Storing the Normalized data ...."

Normalizing cells [---------------------------------------------------------------------------------------------------------------------------------] 10000/4423680 ( 0%) eta: 35m Normalizing cells [----------------------- cannot allocate a vector of 4.6Gb

[jared.andrews07]

That is indeed a memory error. Either run it on a cluster with enough memory or upgrade your workstation. I've never used bigscale, but many data scaling schemes result in dense matrices, which eat up a ton of memory.