prevent nonsensical UMIcounts in case of Smart-seq data (b76b83ec) · Commits · github_fork / ZUMIs

zUMIs-dge2.R

+7 −2

Original line number	Diff line number	Diff line
		@@ -104,8 +104,13 @@ for(i in unique(bccount$chunkID)){
		}
		}

		if(any(unlist(lapply(opt$sequence_files, function(x){grepl("UMI",x$base_definition)} ))) ){
		final<-list( umicount = convert2countM(alldt=allC,what="umicount"),
		readcount = convert2countM(allC,"readcount"))
		}else{
		final<-list(readcount = convert2countM(allC,"readcount"))
		}


		saveRDS(final,file=paste(opt$out_dir,"/zUMIs_output/expression/",opt$project,".dgecounts.rds",sep=""))