updated pipeline to handle the lower limit for empty drops and used t…

…he yml file to param it
cribbslab · Jul 5, 2023 · 8fabdc3 · 8fabdc3
1 parent 7ea87ae
commit 8fabdc3
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diff --git a/scpipelines/seurat/pipeline_qc-1/Rmarkdown/QC.Rmd b/scpipelines/seurat/pipeline_qc-1/Rmarkdown/QC.Rmd
@@ -191,7 +191,7 @@ for(i in 1:length(so)){
     
     # run emptydrops
     set.seed(1)
-    out <- DropletUtils::emptyDrops(assay(sce[[i]], "counts"), lower = 100)
+    out <- DropletUtils::emptyDrops(assay(sce[[i]], "counts"), lower = ini$UMI_filter)
     
     # add emptydrops info to colData
     sce[[i]]@colData$empty_drops_FDR <- out$FDR

diff --git a/scpipelines/seurat/pipeline_qc-1/pipeline.yml b/scpipelines/seurat/pipeline_qc-1/pipeline.yml
@@ -17,7 +17,7 @@ mirror: useast
 so_filter: 100
 
 #Specificy the number of counts if more stringent filter is required
-UMI_filter: 100
+UMI_filter: 300
 
 #Specify the format of output files
 output: seurat_object