Smart3 strandedness (bfafb043) · Commits · github_fork / ZUMIs

README.md

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		@@ -29,6 +29,8 @@ We provide a script to convert zUMIs output into loom file automatically based o
		zUMIs will try to automatically do this, otherwise convert zUMIs output to loom by simply running `Rscript rds2loom.R myRun.yaml`.

		## Changelog
		16 Mar 2020: zUMIs2.7.1: Smart-seq3 data can be run with the proper consideration of strand information. When setting `strand: 1`, UMI reads will use this strand while non-UMI reads will stay unstranded.

		19 Feb 2020: [zUMIs2.7.0 released](https://github.com/sdparekh/zUMIs/releases/tag/2.7.0): Simplify installation greatly by a cond-pack of miniconda with all dependencies. The conda environment is used with `zUMIs-master.sh -c`, with the old behavior staying as the default.

		13 Feb 2020: zUMIs2.6.3: Faster demultiplexing using python/pysam. Made forking of UMI collapse worker threads more robust.

UMIstuffFUN.R

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		@@ -417,6 +417,19 @@ demultiplex_bam <- function(opt, bamfile, nBCs){
		print(Sys.time())
		}

		split_bam <- function(bam, cpu, samtoolsexc){
		UMIbam <- paste0(bam,".UMI.bam")
		internalbam <- paste0(bam,".internal.bam")
		cpus <- floor((cpu-4)/2)
		if(cpus<1){
		cpus <- 2
		}

		cmd_umi <- paste(samtoolsexc, "view -h -@ 2", bam, " \| grep -v -P 'UB:Z:\t' \| ", samtoolsexc, "view -b -@",cpus,"-o",UMIbam,"&")
		cmd_internal <- paste(samtoolsexc, "view -h -@ 2", bam, " \| grep -v 'UB:Z:[A-Z]' \| ", samtoolsexc, "view -b -@",cpus,"-o",internalbam,"&")
		system(paste(cmd_umi,cmd_internal,"wait"))
		return(c(internalbam,UMIbam))
		}

		fixMissingOptions <- function(config){
		if(is.null(config$barcodes$automatic)){

zUMIs-dge2.R

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		@@ -52,6 +52,28 @@ bccount<-splitRG(bccount=bccount, mem= opt$mem_limit)

		saf<-.makeSAF(paste0(opt$out_dir,"/",opt$project,".final_annot.gtf"))
		abamfile<-paste0(opt$out_dir,"/",opt$project,".filtered.tagged.Aligned.out.bam")
		outbamfile <-paste0(opt$out_dir,"/",opt$project,".filtered.Aligned.GeneTagged.bam")

		if(smart3_flag & opt$counting_opts$strand == 1){
		#split bam in UMU ends and internal
		tmp_bams <- split_bam(bam = abamfile, cpu = opt$num_threads, samtoolsexc=samtoolsexc)

		#assign features with appropriate strand
		fnex_int<-.runFeatureCount(tmp_bams[1], saf=saf$exons, strand=0, type="ex", primaryOnly = opt$counting_opts$primaryHit, cpu = opt$num_threads, mem = opt$mem_limit, fcounts_clib = fcounts_clib)
		fnex_umi<-.runFeatureCount(tmp_bams[2], saf=saf$exons, strand=1, type="ex", primaryOnly = opt$counting_opts$primaryHit, cpu = opt$num_threads, mem = opt$mem_limit, fcounts_clib = fcounts_clib)
		ffiles_int <- paste0(fnex_int,".tmp")
		ffiles_umi <- paste0(fnex_umi,".tmp")

		if(opt$counting_opts$introns){
		fnin_int<-.runFeatureCount(ffiles_int, saf=saf$introns, strand=0, type="in", primaryOnly = opt$counting_opts$primaryHit, cpu = opt$num_threads, mem = opt$mem_limit, fcounts_clib = fcounts_clib)
		fnin_umi<-.runFeatureCount(ffiles_umi, saf=saf$introns, strand=1, type="in", primaryOnly = opt$counting_opts$primaryHit, cpu = opt$num_threads, mem = opt$mem_limit, fcounts_clib = fcounts_clib)
		ffiles_int <- paste0(fnin_int,".tmp")
		ffiles_umi <- paste0(fnin_umi,".tmp")
		}
		join_bam_cmd <- paste(samtoolsexc, "cat -o", outbamfile, ffiles_int, ffiles_umi)
		system(join_bam_cmd)
		system(paste0("rm ",tmp_bams[1],"* ",tmp_bams[2],"*"))
		}else{
		fnex<-.runFeatureCount(abamfile,
		saf=saf$exons,
		strand=opt$counting_opts$strand,
		@@ -75,15 +97,15 @@ if(opt$counting_opts$introns){
		ffiles<-paste0(fnin,".tmp")
		}

		system(paste("mv",ffiles,outbamfile))
		}

		if(is.null(opt$mem_limit)){
		mempercpu <- max(round(100/opt$num_threads,0),1)
		}else{
		mempercpu <- max(round(opt$mem_limit/opt$num_threads,0),1)
		}

		outbamfile <-paste0(opt$out_dir,"/",opt$project,".filtered.Aligned.GeneTagged.bam")
		system(paste("mv",ffiles,outbamfile))

		if(opt$counting_opts$Ham_Dist == 0){
		sortbamfile <-paste0(opt$out_dir,"/",opt$project,".filtered.Aligned.GeneTagged.sorted.bam")
		}else{

zUMIs-master.sh

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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=2.7.0b
		vers=2.7.1
		currentv=`curl -s https://raw.githubusercontent.com/sdparekh/zUMIs/master/zUMIs-master.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-------------"; fi

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