GLDS-352_CRA_SS_output_files

The attached filtered gene count data were generated from the snRNAseq (GEX) fastq files hosted on OSDR: https://osdr.nasa.gov/bio/repo/data/studies/OSD-352/7
The following commands were used:
Cell Ranger ARC command:
Used Cellranger Arc 2.0.2 for data processingcellranger-arc count --jobmode=local \
--localcores=32 \
--localmem=115 \
--id=${SAMPLE} \
--reference=/cellranger/refdata-cellranger-arc-mm10-2020-A-2.0.0 \
--libraries=${SAMPLE}_info.csvSTARsolo command:
Used STAR 2.7.10a for data processingSTAR --runThreadN 18 \
--genomeDir $genomeDir \
--soloType CB_UMI_Simple \
--clipAdapterType CellRanger4 \
--outFilterScoreMin 30 \
--soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts \
--soloUMIfiltering MultiGeneUMI_CR \
--soloUMIdedup 1MM_CR \
--soloUMIlen 12 \
--soloCellFilter EmptyDrops_CR $expectedCells 0.99 10 45000 90000 500 0.01 20000 0.01 10000 \
--soloMultiMappers EM \
--outSAMattributes NH HI nM AS CR UR GX GN sS sQ sM \
--outSAMtype BAM Unsorted \
--soloFeatures Gene GeneFull SJ Velocyto \
--readFilesCommand zcat \
--soloCBwhitelist $whitelist \
--outFileNamePrefix $outDir/${sample}/${sample}_ \
--readFilesIn $fastqDir/${sample}_R2_raw.fastq.gz $fastqDir/${sample}_R1_raw.fastq.gz