revert mapping to STAR bam output (bcac30f4) · 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
		23 June 2020: zUMIs2.8.3: Merged code contribution from @gringer: prevent errors by emitting SAM headers in chunked unmapped .bam file output of fqfilter. Changed call to STAR to prevent stalling of samtools pipe.

		18 May 2020: zUMIs2.8.2: Added `merge_demultiplexed_fastq.R` to concatenate previously demultiplexed fastq files. For usage details see here: https://github.com/sdparekh/zUMIs/wiki/Starting-from-demultiplexed-fastq-files

		15 May 2020: zUMIs2.8.1: Smart-seq3 UMI pattern detection now takes one hamming distance error into account.

fqfilter_v2.pl

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		@@ -329,12 +329,12 @@ for (my $i=0; $i<=$#keys; $i++) {
		close $fhTmp;
		}

		if ($filtered == 0) {
		print(STDERR "No reads emitted; please check the parameter file and the warnings above.\n");
		exit;
		} else {
		print(STDERR "reads kept: $filtered; reads discarded: $discarded\n");
		}
		#if ($filtered == 0) {
		# print(STDERR "No reads emitted; please check the parameter file and the warnings above.\n");
		# exit;
		#} else {
		# print(STDERR "reads kept: $filtered; reads discarded: $discarded\n");
		#}

		open BCOUT, '>', $outbcstats \|\| die "Couldn't open file ".$outbcstats.". Check permissions!\n";
		foreach my $bc (keys %bclist) {

zUMIs-mapping.R

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		@@ -77,31 +77,34 @@ cDNA_read_length <- getmode(nchar(cDNA_peek$V1))
		# Setup STAR mapping ------------------------------------------------------
		samtools_load_cores <- ifelse(inp$num_threads>8,2,1)
		avail_cores <- inp$num_threads - samtools_load_cores #reserve threads for samtools file opening
		if(avail_cores < 3){
		cores_samtools <- 1
		cores_star <- 2
		}else{
		cores_samtools <- floor(avail_cores/3)
		cores_star <- avail_cores - cores_samtools
		#if(avail_cores < 3){
		# cores_samtools <- 1
		# cores_star <- 2
		#}else{
		# cores_samtools <- floor(avail_cores/3)
		# cores_star <- avail_cores - cores_samtools
		#}
		if(avail_cores < 2){
		avail_cores = 1
		}

		param_defaults <- paste("--readFilesCommand ",samtools," view -@",samtools_load_cores," --outSAMmultNmax 1 --outFilterMultimapNmax 50 --outSAMunmapped Within --outSAMtype SAM --outStd SAM")
		#param_defaults <- paste("--readFilesCommand ",samtools," view -@",samtools_load_cores," --outSAMmultNmax 1 --outFilterMultimapNmax 50 --outSAMunmapped Within --outSAMtype SAM --outStd SAM")
		param_defaults <- paste("--readFilesCommand ",samtools," view -@",samtools_load_cores," --outSAMmultNmax 1 --outFilterMultimapNmax 50 --outSAMunmapped Within --outSAMtype BAM Unsorted")
		param_misc <- paste("--genomeDir",inp$reference$STAR_index,
		"--sjdbGTFfile",gtf_to_use,
		"--runThreadN",cores_star,
		"--runThreadN",avail_cores,
		"--readFilesIn",paste0(filtered_bams,collapse=","),
		"--outFileNamePrefix",paste(inp$out_dir,"/",inp$project,".filtered.tagged.",sep=""),
		"--sjdbOverhang", cDNA_read_length-1,
		"--readFilesType SAM",inp$read_layout)

		STAR_command <- paste(STAR_exec,param_defaults,param_misc,inp$reference$additional_STAR_params,param_additional_fa)
		if(inp$counting_opts$twoPass==T){
		if(inp$counting_opts$twoPass==TRUE){
		STAR_command <- paste(STAR_command,"--twopassMode Basic")
		}

		samtools_output <- paste0(" \| ",samtools," view -@ ",cores_samtools," -o ",inp$out_dir,"/",inp$project,".filtered.tagged.Aligned.out.bam")

		STAR_command <- paste(STAR_command,samtools_output)
		#samtools_output <- paste0(" \| ",samtools," view -@ ",cores_samtools," -o ",inp$out_dir,"/",inp$project,".filtered.tagged.Aligned.out.bam")
		#STAR_command <- paste(STAR_command,samtools_output)

		#finally, run STAR
		if(inp$which_Stage == "Filtering"){

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=2.8.2
		vers=2.8.3
		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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