prevent warnings (04472a24) · Commits · github_fork / ZUMIs

README.md

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		@@ -23,6 +23,8 @@ You can read more about zUMIs in our [paper](https://doi.org/10.1093/gigascience

		[YAML config Rshiny application](http://shiny.bio.lmu.de:3838/zUMIs-config/)

		Note: zUMIs is compatible with R release 4.0!

		## Loom output
		The loom format is increasing in popularity and compatible with downstream analysis using python out of the box.
		We provide a script to convert zUMIs output into loom file automatically based on the [loomR package from the Satija lab](https://satijalab.org/loomR/loomR_tutorial.html). Please make sure you have loomR installed.

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		@@ -366,7 +366,10 @@ demultiplex_bam <- function(opt, bamfile, nBCs, samtoolsexc, bccount){
		dir.create( paste0(opt$out_dir,"/zUMIs_output/demultiplexed/") )
		}

		installed_py <- try(system("pip freeze", intern = TRUE))
		installed_py <- try(system("pip freeze", intern = TRUE, ignore.stderr = TRUE), silent = TRUE)
		if(grepl('Error', installed_py)){
		installed_py <- try(system("pip3 freeze", intern = TRUE, ignore.stderr = TRUE), silent = TRUE)
		}

		if(any(grepl("pysam==",installed_py))){
		print("Using python implementation to demultiplex.")
		@@ -443,6 +446,7 @@ demultiplex_bam <- function(opt, bamfile, nBCs, samtoolsexc, bccount){
		}else{
		print("Using perl implementation to demultiplex.")
		demux_cmd <- paste0(opt$zUMIs_directory,"/misc/demultiplex_BC.pl ",opt$out_dir," ",opt$project, " ", bamfile, " ", samtoolsexc )
		collect_demultiplex = FALSE
		}
		system(demux_cmd)
		if(collect_demultiplex){

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		@@ -329,7 +329,7 @@ get_gr <- function(y){GenomicRanges::makeGRangesFromDataFrame(y,
		intron.saf <- dplyr::left_join(intron.saf, unique(exon.saf[,c("GeneID","Strand")]), by = c("GeneID"))

		#get intronic bp per gene and intronic reads per gene
		intronGenes <- intron.saf %>% group_by(GeneID) %>% summarize(IntronLengthPerGene = sum(Len), intronsPerGene = length(GeneID))
		intronGenes <- intron.saf %>% group_by(GeneID) %>% summarize(IntronLengthPerGene = sum(Len), intronsPerGene = length(GeneID), .groups = "drop")

		saf <- list(introns = unique(intron.saf), exons = unique(exon.saf), intronsPerGene = intronGenes,intergenicBp = intergenicBp)

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		@@ -3,7 +3,7 @@
		# Pipeline to run UMI-seq analysis from fastq to read count tables.
		# Authors: Swati Parekh, Christoph Ziegenhain, Beate Vieth & Ines Hellmann
		# Contact: sparekh@age.mpg.de or christoph.ziegenhain@ki.se
		vers=2.9.3d
		vers=2.9.3e
		currentv=$(curl -s https://raw.githubusercontent.com/sdparekh/zUMIs/main/zUMIs.sh \| grep '^vers=' \| cut -f2 -d "=")
		if [ "$currentv" != "$vers" ] ; then
		echo -e "------------- \n\n Good news! A newer version of zUMIs is available at https://github.com/sdparekh/zUMIs \n\n-------------";