minor bug fix for SmartSeq3 test (44b67ea3) · Commits · github_fork / Universc

launch_universc.sh

+27 −24

Original line number	Diff line number	Diff line
		@@ -20,7 +20,7 @@
		install=false

		######UniverSC version#####
		universcversion="1.1.1"
		universcversion="1.1.3"
		##########


		@@ -64,8 +64,11 @@ fi
		echo "Running launch_universc.sh in '$SDIR'"

		TOOLS=${SDIR}/sub
		ADDMOCKUMI=${TOOLS}/AddMockUMI.pl
		BARCODERECOVER=${TOOLS}/RecoverBarcodes.pl
		MAKEINDROPBARCODES=${TOOLS}/MakeIndropBarcodes.pl
		FILTERSMARTSEQREADUMI=${TOOLS}/FilterSmartSeqReadUMI.pl
		CONCATENATEBARCODES=${TOOLS}/ConcatenateDualIndexBarcodes.pl
		PERCELLSTATS=${TOOLS}/ExtractBasicStats.pl
		##########

		@@ -1752,7 +1755,7 @@ else
		fi
		elif [[ "$technology" == "bravo" ]]; then
		barcodefile=${whitelistdir}/KAPA_UDI_dual_barcodes.txt
		if [[ ! -f ${whitelistdir}/KAPA_UDI_dual_barcodes.txt
		if [[ ! -f ${whitelistdir}/KAPA_UDI_dual_barcodes.txt ]]; then
		echo " ...generating combination of I1, I2, and RT barcodes..."
		fi
		elif [[ "$technology" == "fluidigm-c1" ]] \|\| [[ "$technology" == "c1-cage" ]] \|\| [[ "$technology" == "ramda-seq" ]] \|\| [[ "$technology" == "c1-ramda-seq" ]]; then
		@@ -2724,12 +2727,12 @@ else

		echo " ...concatencate barcodes to R1 from I1 and I2 index files"
		# concatenate barcocdes from index to R1 as (bases 1-16 of the) barcode, moving (read to start at base 17-)
		perl sub/ConcatenateDualIndexBarcodes.pl --additive=${convI1} --additive=${convI2} --ref_fastq=${convR1} --out_dir $crIN
		perl ${CONCATENATEBARCODES} --additive ${convI1} --additive ${convI2} --ref_fastq ${convR1} --out_dir $crIN
		else
		barcodelength=$indexlength
		echo " ...concatencate barcodes to R1 from I1 index files"
		# concatenate barcocdes from index to R1 as (bases 1-6 of the) barcode, moving (read to start at base 7-)
		perl sub/ConcatenateDualIndexBarcodes.pl --additive=${convI1} --ref_fastq=${convR1} --out_dir $crIN
		perl ${CONCATENATEBARCODES} --additive ${convI1} --ref_fastq ${convR1} --out_dir $crIN
		fi

		#returns a combined R1 file with I1-R1 concatenated (I1 is cell barcode)
		@@ -2740,7 +2743,7 @@ else
		echo "adding mock UMI"
		fi
		# add mock UMI (count reads instead of UMI) barcodelength=6, umi_default=10
		perl sub/AddMockUMI.pl --fastq=${convR1} --out_dir $crIN --head_length=$barcodelength --umi_length=$umi_default
		perl ${ADDMOCKUMI} --fastq ${convR1} --out_dir $crIN --head_length $barcodelength --umi_length $umi_default
		umilength=$umi_default
		umiadjust=0
		if [[ $chemistry == "SC3Pv3" ]]; then
		@@ -2799,7 +2802,7 @@ else
		# filter UMI reads by matching tag sequence ATTGCGCAATG (bases 1-11 of R1) and remove as an adapters

		#same as SmartSeq2
		perl sub/FilterSmartSeqReadUMI.pl --r1=${convR1} --r2=${convR2} --tag="AAGCAGTGGTATCAACGCAGAGTAC" --out_dir $crIN
		perl ${FILTERSMARTSEQREADUMI} --r1 ${convR1} --r2 ${convR2} --tag 'AAGCAGTGGTATCAACGCAGAGTAC' --out_dir $crIN
		echo " ...trim tag sequence from R1"

		# returns R1 with tag sequence removed (left trim) starting with 8pbp UMI and corresponding reads for I1, I2, and R2
		@@ -2831,7 +2834,7 @@ else
		echo "adding mock UMI"
		fi
		# add mock UMI (count reads instead of UMI) barcodelength=10 or 11, umi_default=10 <- default for "icell8-5-prime" and "icell8-full-length"
		perl sub/AddMockUMI.pl --fastq=${convR1} --out_dir $crIN --head_length=$barcodelength --umi_length=$umi_default
		perl ${ADDMOCKUMI} --fastq ${convR1} --out_dir $crIN --head_length $barcodelength --umi_length $umi_default
		umilength=$umi_default
		umiadjust=0
		if [[ $chemistry == "SC3Pv3" ]]; then
		@@ -2934,7 +2937,7 @@ else
		echo " ...concatencate barcodes to R1 from I1 index file"
		# concatenate barcocdes from dual indexes to R1 as (bases 1-8 of the) barcode (bases 1-16), moving UMI to (17-22)
		# filter UMI reads by matching tag sequence ATTGCGCAATG (bases 1-11 of R1) and remove as an adapters
		perl sub/ConcatenateDualIndexBarcodes.pl --additive=${convI1} --ref_fastq=${convR1} --out_dir $crIN
		perl ${CONCATENATEBARCODES} --additive ${convI1} --ref_fastq ${convR1} --out_dir $crIN

		#returns a combined R1 file with I1-I2-R1 concatenated (I1 and I2 are R1 barcode)
		mv $crIN/Concatenated_File.fastq ${convR1}
		@@ -3015,7 +3018,7 @@ else
		echo " ...concatencate barcodes to R1 from I1 and I2 index files"
		# concatenate barcocdes from dual indexes to R1 as (bases 1-20 of the) barcode, moving RT barcode (21-30) UMI to (31-38)
		# filter UMI reads by matching tag sequence ATTGCGCAATG (bases 1-11 of R1) and remove as an adapters
		perl sub/ConcatenateDualIndexBarcodes.pl --additive=${convI1} --additive=${convI2} --ref_fastq=${convR1} --out_dir $crIN
		perl ${CONCATENATEBARCODES} --additive ${convI1} --additive ${convI2} --ref_fastq ${convR1} --out_dir ${crIN}

		#returns a combined R1 file with I1-I2-R1 concatenated (I1 and I2 are R1 barcode)
		mv $crIN/Concatenated_File.fastq ${convR1}
		@@ -3067,7 +3070,7 @@ else
		echo " ...concatencate barcodes to R1 from I1 and I2 index files"
		# concatenate barcocdes from dual indexes to R1 as (bases 1-20 of the) barcode, moving RT barcode (21-30) UMI to (31-38)
		# filter UMI reads by matching tag sequence ATTGCGCAATG (bases 1-11 of R1) and remove as an adapters
		perl sub/ConcatenateDualIndexBarcodes.pl --additive=${convI1} --additive=${convI2} --ref_fastq=${convR1} --out_dir $crIN
		perl ${CONCATENATEBARCODES} --additive ${convI1} --additive ${convI2} --ref_fastq ${convR1} --out_dir ${crIN}

		#returns a combined R1 file with I1-I2-R1 concatenated (I1 and I2 are R1 barcode)
		mv $crIN/Concatenated_File.fastq ${convR1}
		@@ -3107,7 +3110,7 @@ else
		echo " ...concatencate 10x ATAC barcodes to R1 from I2 index files"
		# concatenate barcocdes from dual indexes to R1 as (bases 1-16 of the 27 bp) barcode, moving RT barcode (17-27) UMI to (28-35)
		# filter UMI reads by matching tag sequence ATTGCGCAATG (bases 1-11 of R1) and remove as an adapters
		perl sub/ConcatenateDualIndexBarcodes.pl --additive=${convI2} --ref_fastq=${convR1} --out_dir $crIN
		perl ${CONCATENATEBARCODES} --additive ${convI2} --ref_fastq ${convR1} --out_dir ${crIN}

		#returns a combined R1 file with I1-I2-R1 concatenated (I1 and I2 are R1 barcode)
		mv $crIN/Concatenated_File.fastq ${convR1}
		@@ -3129,8 +3132,8 @@ else
		if [[ "$technology" == "strt-seq" ]]; then
		# add mock UMI (count reads instead of UMI) barcodelength=6, umi_default=10
		echo " ...generate mock UMI for compatibility"
		perl sub/AddMockUMI.pl --fastq=${convR1} --out_dir $crIN --head_length=$barcodelength --umi_length=$umi_default
		umilength=$umi_default
		perl ${ADDMOCKUMI} --fastq ${convR1} --out_dir ${crIN} --head_length ${barcodelength} --umi_length ${umi_default}
		umilength=${umi_default}
		umiadjust=0
		chemistry="SC5P-PE"

		@@ -3143,7 +3146,7 @@ else
		chemistry="SC5P-R1"
		echo " ...concatencate barcodes to R1 from I1 index files"
		# concatenate barcocdes from I1 index to R1 as barcode (bases 1-8)
		perl sub/ConcatenateDualIndexBarcodes.pl --additive=${convI1} --ref_fastq=${convR1} --out_dir $crIN
		perl ${CONCATENATEBARCODES} --additive ${convI1} --ref_fastq ${convR1} --out_dir ${crIN}
		fi
		if [[ "$technology" == "strt-seq-2i" ]]; then
		convI1=$(echo $read \| perl -pne 's/(.*)_R1/$1_I1/' )
		@@ -3151,11 +3154,11 @@ else
		chemistry="SC5P-R1"
		echo " ...concatencate barcodes to R1 from I1 and I2index files"
		# concatenate barcocdes from I1 index to R1 as barcode (bases 1-8)
		perl sub/ConcatenateDualIndexBarcodes.pl --additive=${convI1} --additive=${convI2} --ref_fastq=${convR1} --out_dir $crIN
		perl ${CONCATENATEBARCODES} --additive ${convI1} --additive ${convI2} --ref_fastq ${convR1} --out_dir ${crIN}
		fi

		#convert TSO to expected length for 10x 5' (TSS in R1 from base 39)
		echo " handling $convFile ..."
		echo " handling ${convFile} ..."
		tsoS="TTTCTTATATGGG"
		tsoQ="IIIIIIIIIIIII"
		#Add 10x TSO characters to the end of the sequence
		@@ -3274,7 +3277,7 @@ else
		echo " ...remove internal reads for ${technology} by matching TSO sequence for UMI reads"
		# filter UMI reads by matching tag sequence ATTGCGCAATG (bases 1-11 of R1) and remove as an adapters

		perl sub/FilterSmartSeqReadUMI.pl --r1=${convR1} --r2=${convR2} --i1=${convI1} --i2=${convI2} --tag="AAGCAGTGGTATCAACGCAGAGTAC" --out_dir $crIN
		perl ${FILTERSMARTSEQREADUMI} --r1 ${convR1} --r2 ${convR2} --i1 ${convI1} --i2 ${convI2} --tag 'AAGCAGTGGTATCAACGCAGAGTAC' --out_dir ${crIN}
		echo " ...trim tag sequence from R1"

		# returns R1 with tag sequence removed (left trim) starting with 8pbp UMI and corresponding reads for I1, I2, and R2
		@@ -3285,15 +3288,15 @@ else

		echo " ...concatencate barcodes to R1 from I1 and I2 index files"
		# concatenate barcocdes from dual indexes to R1 as barcode (bases 1-16)
		perl sub/ConcatenateDualIndexBarcodes.pl --additive=${convI1} --additive=${convI2} --ref_fastq=${convR1} --out_dir $crIN
		perl ${CONCATENATEBARCODES} --additive ${convI1} --additive ${convI2} --ref_fastq ${convR1} --out_dir ${crIN}

		#returns a combined R1 file with I1-I2-R1 concatenated (I1 and I2 are R1 barcode)
		## 16 bp barcode, GGG for TSO, no UMI
		mv $crIN/Concatenated_File.fastq ${convR1}

		# add mock UMI (count reads instead of UMI) barcodelength=16, umi_default=10
		perl sub/AddMockUMI.pl --fastq=${convR1} --out_dir $crIN --head_length=$barcodelength --umi_length=$umi_default
		umilength=$umi_default
		perl ${ADDMOCKUMI} --fastq ${convR1} --out_dir ${crIN} --head_length ${barcodelength} --umi_length ${umi_default}
		umilength=${umi_default}
		umiadjust=0
		chemistry="SC3Pv2"

		@@ -3340,7 +3343,7 @@ else

		echo " ...remove internal for ${technology} by matching tag sequence for UMI reads"
		# filter UMI reads by matching tag sequence ATTGCGCAATG (bases 1-11 of R1) and remove as an adapters
		perl sub/FilterSmartSeqReadUMI.pl --r1=${convR1} --r2=${convR2} --i1=${convI1} --i2=${convI2} --tag="ATTGCGCAATG" --out_dir=$crIN
		perl ${FILTERSMARTSEQREADUMI} --r1 ${convR1} --r2 ${convR2} --i1 ${convI1} --i2 ${convI2} --tag 'ATTGCGCAATG' --out_dir ${crIN}
		echo " ...trim tag sequence from R1"

		# returns R1 with tag sequence removed (left trim) starting with 8pbp UMI and corresponding reads for I1, I2, and R2
		@@ -3351,7 +3354,7 @@ else

		echo " ...concatencate barcodes to R1 from I1 and I2 index files"
		# concatenate barcocdes from dual indexes to R1 as barcode (bases 1-16)
		perl sub/ConcatenateDualIndexBarcodes.pl --additive=${convI1} --additive=${convI2} --ref_fastq=${convR1} --out_dir=$crIN
		perl ${CONCATENATEBARCODES} --additive ${convI1} --additive ${convI2} --ref_fastq ${convR1} --out_dir ${crIN}

		#returns a combined R1 file with I1-I2-R1 concatenated (I1 and I2 are R1 barcode)
		mv $crIN/Concatenated_File.fastq ${convR1}
		@@ -3428,7 +3431,7 @@ else
		if [[ $chemistry == "SC3Pv3" ]]; then
		chemistry="SC3Pv2"
		fi
		perl sub/AddMockUMI.pl --fastq=${convR1} --out_dir $crIN --head_length=$barcodelength --umi_length=$umi_default
		perl ${ADDMOCKUMI} --fastq ${convR1} --out_dir $crIN --head_length ${barcodelength} --umi_length ${umi_default}
		umilength=$umi_default
		umiadjust=0
		if [[ $chemistry == "SC3Pv3" ]]; then

sub/ConcatenateDualIndexBarcodes.pl

+2 −2

Original line number	Diff line number	Diff line
		@@ -27,7 +27,7 @@ my $out_dir = "";
		#making the options into external arguments.
		GetOptions (
		'ref_fastq=s' => \$ref_fastq,
		'additives=s' => \@additives,
		'additive=s' => \@additives,
		'out_dir=s' => \$out_dir
		);

		@@ -36,7 +36,7 @@ if (!$ref_fastq) {
		die "USAGE: option --ref_fastq <Reference.fastq> is required.\n";
		}
		elsif (scalar @additives < 1) {
		die "USAGE: option --additives <additional.fastq> is required.\n";
		die "USAGE: option --additive <additional.fastq> is required.\n";
		}
		elsif (!$out_dir) {
		die "USAGE: option --out_dir <OUTPUT_DIRECTORY> is required.\n";

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