Local UCSC cell browser usage for Seurat¶
Notes¶
An important step is to give the markers to misc attribute. merged_obj@misc$markers <- markers
so that the program can automatically know the cluster markers.
Idents(object = merged_obj) <- merged_obj@meta.data$'manual_label'
markers <- FindAllMarkers(merged_obj, min.pct = 0.2, logfc.threshold = 0.2)
merged_obj@misc$markers <- markers
saveRDS(merged_obj, "merged_obj.rds")
Usage¶
module load conda3/202011
source activate /home/yli11/.conda/envs/captureC
cbImportSeurat -i merged_obj.rds -o merged_obj_CB # it will take a while
# I usually modify the configuration file to use the log normalized counts, instead of raw counts
# nano cellbrowser.conf
# exprMatrix="data_exprMatrix.tsv.gz"
cd merged_obj_CB
bsub -q standard -P Genomics -R 'rusage[mem=20000]' -J CB cbBuild -o ./CB_cells/ -p 8051