custom fastq/mapped bam file (09ba2352) · Commits · github_fork / ZUMIs

zUMIs-dge.R

+13 −1

Original line number	Diff line number	Diff line
		@@ -45,11 +45,17 @@ paks<-lapply(packages, function(x) suppressMessages(require(x, character.only =
		rm(paks)

		# Check the version of Rsubread
		bla<-data.frame(installed.packages()[grep("Rsubread",installed.packages()),c("LibPath","Version")],row.names = NULL)
		if(length(grep("Rsubread",installed.packages()))==1){
		bla<-data.frame(t(installed.packages()[grep("Rsubread",installed.packages()),c("LibPath","Version")]),row.names = NULL)
		}else{
		bla<-data.frame((installed.packages()[grep("Rsubread",installed.packages()),c("LibPath","Version")]),row.names = NULL)
		}


		if(length(grep("Rsubread",installed.packages()))==0){
		print("I did not find Rsubread so I am installing it...")
		install.packages("https://bioarchive.galaxyproject.org/Rsubread_1.26.0.tar.gz", repos = NULL, type = "source")
		bla<-data.frame(t(installed.packages()[grep("Rsubread",installed.packages()),c("LibPath","Version")]),row.names = NULL)
		library("Rsubread", lib.loc=as.character(bla[bla$Version %in% "1.26.0", "LibPath"]))

		}else{
		@@ -57,9 +63,15 @@ if(length(grep("Rsubread",installed.packages()))==0){
		if(installed.packages()[grep("Rsubread",installed.packages()),"Version"] != "1.26.0"){
		print("I need Rsubread 1.26.0 so I am installing it...")
		install.packages("https://bioarchive.galaxyproject.org/Rsubread_1.26.0.tar.gz", repos = NULL, type = "source")
		bla<-data.frame((installed.packages()[grep("Rsubread",installed.packages()),c("LibPath","Version")]),row.names = NULL)
		library("Rsubread", lib.loc=as.character(bla[bla$Version %in% "1.26.0", "LibPath"]))
		}else{
		print("I am loading Rsubread 1.26.0...")
		if(length(grep("Rsubread",installed.packages()))==1){
		bla<-data.frame(t(installed.packages()[grep("Rsubread",installed.packages()),c("LibPath","Version")]),row.names = NULL)
		}else{
		bla<-data.frame((installed.packages()[grep("Rsubread",installed.packages()),c("LibPath","Version")]),row.names = NULL)
		}
		library("Rsubread", lib.loc=as.character(bla[bla$Version %in% "1.26.0", "LibPath"]))
		}

zUMIs-master.sh

+54 −2

Original line number	Diff line number	Diff line
		@@ -63,6 +63,14 @@ Make sure you have 3-4 times more disk space to your input fastq files.
		-e <STAR-executable> : path to STAR executable in your system. Default: STAR
		-t <samtools-executable>: path to samtools executable in your system. Default: samtools
		-i <zUMIs-dir> : Directory containing zUMIs scripts. Default: path to this script.

		## zUMIs from any stage ##
		-A <isCustomFASTQ> : yes/no. Start zUMIs from Mapping stage with your own FASTQ files if you don't want to use zUMIs filter.
		Only works with -w Mapping.
		Make sure to provide the Required parameters. Default: no.
		-X <CustomMappedBAM> : Mapped BAM file. Start zUMIs from Counting stage with your own BAM file if you don't want to use STAR.
		Only works with -w Counting.
		Make sure to provide the Required parameters. Default: NA.
		-w <whichStage> : Start zUMIs from <-w TEXT> stage. Possible TEXT(Filtering, Mapping, Counting, Summarising). Default: Filtering.
		Make sure to give the same <outputdir> (-o) and <StudyName> (-n) if you start from the middle stage.
		zUMIs has a defined directory structure.
		@@ -95,13 +103,17 @@ zumisdir=$(dirname `readlink -f $0`)
		whichStage=filtering
		isstrt=no
		bcread2=NA
		CustomMappedBAM=NA
		isCustomFASTQ=no
		BaseTrim=3
		xcrange2=0-0

		while getopts ":R:S:f:r:g:o:a:t:s:c:m:l:b:n:q:Q:z:u:x:e:p:i:d:w:j:F:C:y:h" options; do #Putting <:> between keys implies that they can not be called without an argument.
		while getopts ":R:S:f:r:g:o:a:t:s:c:m:l:b:n:q:Q:z:u:x:e:p:i:d:X:A:w:j:F:C:y:h" options; do #Putting <:> between keys implies that they can not be called without an argument.
		case $options in
		R ) isslurm=$OPTARG;;
		S ) isStats=$OPTARG;;
		X ) isCustomFASTQ=$OPTARG;;
		A ) isCustomFASTQ=$OPTARG;;
		w ) whichStage=$OPTARG;;
		f ) bcread=$OPTARG;;
		r ) cdnaread=$OPTARG;;
		@@ -142,6 +154,7 @@ if [[ $OPTIND -eq 1 ]] ; then
		fi

		isslurm=`echo "$isslurm" \| tr '[:upper:]' '[:lower:]'` # convert to all lower case
		isCustomFASTQ=`echo "$isCustomFASTQ" \| tr '[:upper:]' '[:lower:]'` # convert to all lower case
		isStats=`echo "$isStats" \| tr '[:upper:]' '[:lower:]'` # convert to all lower case
		isstrt=`echo "$isstrt" \| tr '[:upper:]' '[:lower:]'` # convert to all lower case
		whichStage=`echo "$whichStage" \| tr '[:upper:]' '[:lower:]'` # convert to all lower case
		@@ -182,6 +195,8 @@ echo -e "\n\n You provided these parameters:
		SLURM workload manager: $isslurm
		Summary Stats to produce: $isStats
		Start the pipeline from: $whichStage
		A custom mapped BAM: $CustomMappedBAM
		Custom filtered FASTQ: $isCustomFASTQ
		Barcode read: $bcread
		cDNA read: $cdnaread
		Study/sample name: $sname
		@@ -214,6 +229,12 @@ echo -e "\n\n You provided these parameters:
		[ -d $outdir/zUMIs_output/stats ] \|\| mkdir $outdir/zUMIs_output/stats
		[ -d $outdir/zUMIs_output/filtered_fastq ] \|\| mkdir $outdir/zUMIs_output/filtered_fastq

		if [[ "$CustomMappedBAM" != "NA" ]] ; then
		whichStage=counting
		fi
		if [[ "$isCustomFASTQ" != "no" ]] ; then
		whichStage=mapping
		fi
		#Submit all the jobs
		if [[ "$isslurm" == "yes" ]] ; then
		case "$whichStage" in
		@@ -229,12 +250,43 @@ if [[ "$isslurm" == "yes" ]] ; then
		bash $zumisdir/zUMIs-cleaning.sh $sname $outdir
		;;
		"mapping")
		if [[ "$isCustomFASTQ" == "yes" ]] ; then
		if [[ $cdnaread =~ \.gz$ ]] ; then
		ln -s $cdnaread $outdir/$sname.cdnaread.filtered.fastq.gz
		else
		pigz -c -p $threads $cdnaread > $outdir/$sname.cdnaread.filtered.fastq.gz
		fi
		if [[ $bcread =~ \.gz$ ]] ; then
		ln -s $bcread $outdir/$sname.barcoderead.filtered.fastq.gz
		else
		pigz -c -p $threads $bcread > $outdir/$sname.barcoderead.filtered.fastq.gz
		fi
		bash $zumisdir/zUMIs-prep.sh $outdir/$sname.barcoderead.filtered.fastq.gz $outdir/$sname.cdnaread.filtered.fastq.gz $sname $outdir $zumisdir
		fi
		bash $zumisdir/zUMIs-mapping.sh $sname $outdir $genomedir $gtf $threads $readlen "$starparams" $starexc $samtoolsexc $xmrange $BaseTrim $isstrt
		bash $zumisdir/zUMIs-prepCounting.sh $sname $outdir $threads $samtoolsexc
		bash $zumisdir/zUMIs-counting.sh $sname $outdir $barcodes $threads $gtf $strandedness $xcrange $xmrange $subsampling $zumisdir $isStats $whichStage $isstrt $bcread2 $xcrange2
		bash $zumisdir/zUMIs-cleaning.sh $sname $outdir
		;;
		"counting")
		if [[ "$CustomMappedBAM" != "NA" ]] ; then
		if [[ $cdnaread =~ \.gz$ ]] ; then
		ln -s $cdnaread $outdir/$sname.cdnaread.filtered.fastq.gz
		else
		pigz -c -p $threads $cdnaread > $outdir/$sname.cdnaread.filtered.fastq.gz
		fi
		if [[ $bcread =~ \.gz$ ]] ; then
		ln -s $bcread $outdir/$sname.barcoderead.filtered.fastq.gz
		else
		pigz -c -p $threads $bcread > $outdir/$sname.barcoderead.filtered.fastq.gz
		fi
		bash $zumisdir/zUMIs-prep.sh $outdir/$sname.barcoderead.filtered.fastq.gz $outdir/$sname.cdnaread.filtered.fastq.gz $sname $outdir $zumisdir
		fi

		if [[ ! -f $outdir/$sname.barcodelist.filtered.sort.sam ]] ; then
		bash $zumisdir/zUMIs-prepCounting.sh $sname $outdir $threads $samtoolsexc
		fi

		bash $zumisdir/zUMIs-counting.sh $sname $outdir $barcodes $threads $gtf $strandedness $xcrange $xmrange $subsampling $zumisdir $isStats $whichStage $isstrt $bcread2 $xcrange2
		bash $zumisdir/zUMIs-cleaning.sh $sname $outdir
		;;
		@@ -244,6 +296,6 @@ if [[ "$isslurm" == "yes" ]] ; then
		;;
		esac
		else
		bash $zumisdir/zUMIs-noslurm.sh $cdnaread $bcread $sname $outdir $xcrange $xmrange $cbasequal $mbasequal $molbcbase $cellbcbase $threads $genomedir $gtf $readlen "$starparams" $starexc $barcodes $strandedness $subsampling $zumisdir $samtoolsexc $isStats $whichStage $bcread2 $BaseTrim $isstrt $xcrange2
		bash $zumisdir/zUMIs-noslurm.sh $cdnaread $bcread $sname $outdir $xcrange $xmrange $cbasequal $mbasequal $molbcbase $cellbcbase $threads $genomedir $gtf $readlen "$starparams" $starexc $barcodes $strandedness $subsampling $zumisdir $samtoolsexc $isStats $whichStage $bcread2 $BaseTrim $isstrt $xcrange2 $CustomMappedBAM $isCustomFASTQ
		fi

zUMIs-noslurm.sh

+35 −1

Original line number	Diff line number	Diff line
		@@ -28,6 +28,8 @@ f3="${24}"
		bt="${25}"
		isstrt="${26}"
		xc2="${27}"
		CustomMappedBAM="${28}"
		isCustomFASTQ="${29}"

		if [[ "$isstrt" == "no" ]] ; then
		rl=`expr $r - 1`
		@@ -80,6 +82,20 @@ re='^[0-9]+$'
		fi
		;;
		"mapping")
		if [[ "$isCustomFASTQ" == "yes" ]] ; then
		if [[ $f1 =~ \.gz$ ]] ; then
		ln -s $f1 $o/$sn.cdnaread.filtered.fastq.gz
		else
		pigz -c -p $t $f1 > $o/$sn.cdnaread.filtered.fastq.gz
		fi
		if [[ $f2 =~ \.gz$ ]] ; then
		ln -s $f2 $o/$sn.barcoderead.filtered.fastq.gz
		else
		pigz -c -p $t $f2 > $o/$sn.barcoderead.filtered.fastq.gz
		fi
		perl $zumisdir/fqcheck.pl $o/$sn.barcoderead.filtered.fastq.gz $o/$sn.cdnaread.filtered.fastq.gz $sn $o $zumisdir
		fi

		$starexc --genomeDir $g --runThreadN $t --readFilesCommand zcat --sjdbGTFfile $gtf --outFileNamePrefix $o/$sn. --outSAMtype BAM Unsorted --outSAMmultNmax 1 --outFilterMultimapNmax 50 --outSAMunmapped Within --sjdbOverhang $rl --twopassMode Basic --readFilesIn $o/$sn.cdnaread.filtered.fastq.gz $x

		$samtoolsexc sort -n -O bam -T temp.$sn -@ $t -m 2G -o $o/$sn.aligned.sorted.bam $o/$sn.Aligned.out.bam
		@@ -99,9 +115,27 @@ re='^[0-9]+$'
		fi
		;;
		"counting")
		if [[ "$CustomMappedBAM" != "NA" ]] ; then
		if [[ $f1 =~ \.gz$ ]] ; then
		ln -s $f1 $o/$sn.cdnaread.filtered.fastq.gz
		else
		pigz -c -p $t $f1 > $o/$sn.cdnaread.filtered.fastq.gz
		fi
		if [[ $f2 =~ \.gz$ ]] ; then
		ln -s $f2 $o/$sn.barcoderead.filtered.fastq.gz
		else
		pigz -c -p $t $f2 > $o/$sn.barcoderead.filtered.fastq.gz
		fi
		perl $zumisdir/fqcheck.pl $o/$sn.barcoderead.filtered.fastq.gz $o/$sn.cdnaread.filtered.fastq.gz $sn $o $zumisdir
		fi

		ln -s -f $o/$sn.aligned.sorted.bam "$o/$sn.aligned.sorted.bam.in"
		ln -s -f $o/$sn.aligned.sorted.bam $o/$sn.aligned.sorted.bam.ex

		if [[ ! -f $o/$sn.barcodelist.filtered.sort.sam ]] ; then
		$samtoolsexc sort -n -O sam -T tmp.$sn -@ $t -m 2G -o $o/$sn.barcodelist.filtered.sort.sam $o/$sn.barcodelist.filtered.sam
		fi

		if [[ $bn =~ $re ]] ; then
		Rscript $zumisdir/zUMIs-dge.R --gtf $gtf --abam $o/$sn.aligned.sorted.bam --ubam $o/$sn.barcodelist.filtered.sort.sam --barcodenumber $bn --out $o --sn $sn --cores $t --strandedness $stra --bcstart $xcst --bcend $xcend --umistart $xmst --umiend $xmend --subsamp $subs
		else

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