Merge branch 'dev' of github.com:TomKellyGenetics/universc into dev (29582552) · Commits · github_fork / Universc

.gitattributes

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	@@ -59,3 +59,8 @@ test/shared/smartseq3-test/Smartseq3_diySpike_R1.fastq.gz filter=lfs diff=lfs me
	test/shared/smartseq3-test/Smartseq3_diySpike_R2.fastq.gz filter=lfs diff=lfs merge=lfs -text		test/shared/smartseq3-test/Smartseq3_diySpike_R2.fastq.gz filter=lfs diff=lfs merge=lfs -text
	test/shared/sciseq-v3-test/SRR7827205_S1_R1.fastq.gz filter=lfs diff=lfs merge=lfs -text		test/shared/sciseq-v3-test/SRR7827205_S1_R1.fastq.gz filter=lfs diff=lfs merge=lfs -text
	test/shared/sciseq-v3-test/SRR7827205_S1_R2.fastq.gz filter=lfs diff=lfs merge=lfs -text		test/shared/sciseq-v3-test/SRR7827205_S1_R2.fastq.gz filter=lfs diff=lfs merge=lfs -text
			test/shared/icell8-test/72618_KU812_L002_R2_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
			test/shared/cellranger-tiny-fastq/1.2.0/read-RA_si-TTTCATGA_lane-008-chunk-001.fastq.gz filter=lfs diff=lfs merge=lfs -text
			test/shared/icell8-test/72618_KU812_L001_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
			test/shared/icell8-test/72618_KU812_L001_R2_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
			test/shared/icell8-test/72618_KU812_L002_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text

launch_universc.sh

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test/shared/icell8-test/72618_KU812_L002_R1_001.fastq.gz

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test/shared/icell8-test/72618_KU812_L002_R2_001.fastq.gz

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	@@ -3018,7 +3018,7 @@ else

	echo " ...remove internal for ${technology} by matching tag sequence for UMI reads"		echo " ...remove internal for ${technology} by matching tag sequence for UMI reads"
	# filter UMI reads by matching tag sequence ATTGCGCAATG (bases 1-11 of R1) and remove as an adapters		# filter UMI reads by matching tag sequence ATTGCGCAATG (bases 1-11 of R1) and remove as an adapters
	perl sub/FilterSmartSeqReadUMI.pl --r1=${convR1} --r2=${convR2} --i1=${convI1} --i2=${convI2} --out_dir=$crIN --tag=		perl sub/FilterSmartSeqReadUMI.pl --r1=${convR1} --r2=${convR2} --i1=${convI1} --i2=${convI2} --tag="ATTGCGCAATG" --out_dir=$crIN
	echo " ...trim tag sequence from R1"		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		# returns R1 with tag sequence removed (left trim) starting with 8pbp UMI and corresponding reads for I1, I2, and R2
	@@ -3029,8 +3029,13 @@ else

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

			=======
			perl sub/ConcatenateDualIndexBarcodes.pl --additive=${convI1} --additive=${convI2} --ref_fastq=${convR1} --out_dir=$crIN

			>>>>>>> c38e32ea3cb07d74951b60e666b6885377f7b77a
	#returns a combined R1 file with I1-I2-R1 concatenated (I1 and I2 are R1 barcode)		#returns a combined R1 file with I1-I2-R1 concatenated (I1 and I2 are R1 barcode)
	mv $crIN/Concatenated_File.fastq ${convR1}		mv $crIN/Concatenated_File.fastq ${convR1}

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