I have raw data from 10x single cell RNA seq v3. Both R1 and R2 are fastq.gz files, each has a size about 20G.
I was running STARSolo by following the https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/scrna-preprocessing-tenx/tutorial.html
“Input Type”: Paired collection of barcode and cDNA reads param-file “Collection of Pairs”: the name of your paired collection param-file “RNA-Seq Cell Barcode Whitelist”: 3M-february-2018.txt.gz “Custom or built-in reference genome”: Use a built-in index “Reference genome with or without an annotation”: use genome reference without builtin gene-model “Select reference genome”: Human (Homo Sapiens): hg19 Full “Gene model (gff3,gtf) file for splice junctions”: Homo_sapiens.GRCh37.75.gtf In “Advanced Settings”: “Configure Chemistry Options”: Cell Ranger v3
l I got the three files, genes, barcodes and matrix. And then I was trying to follow the Seurat instruction on R as follows:
But however, in Seurat, I only got 43 cells and was unable to run dimentional reduction
RunPCA(), pbmc <- RunPCA(pbmc, features = VariableFeatures(object = pbmc))
because the default number of npcs(number of PCs) is 50, then I reduced to 14 15 40 and tried to cluster the cells, however, I only got one cluster.
I am wondering if anyone has the same problem with me? Thank you so much.
note: I didn't pair my R1 and R2 files, I uploaded them separately, I think this is a case. I was re-running it with the paired file(paired R1 and R2 raw data), now I got much more larger output than the first time, I think this time will be better, I will see it. The problem has been solved.