From 8fabdc3aeec9103f30637b789f106f7bb0103dbf Mon Sep 17 00:00:00 2001 From: ECRWatson Date: Wed, 5 Jul 2023 14:02:09 +0100 Subject: [PATCH] updated pipeline to handle the lower limit for empty drops and used the yml file to param it --- scpipelines/seurat/pipeline_qc-1/Rmarkdown/QC.Rmd | 2 +- scpipelines/seurat/pipeline_qc-1/pipeline.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/scpipelines/seurat/pipeline_qc-1/Rmarkdown/QC.Rmd b/scpipelines/seurat/pipeline_qc-1/Rmarkdown/QC.Rmd index ee8c03b..f816d6b 100755 --- 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 index 7946012..ae16a61 100644 --- 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