correct automated indexes and Smart-Seq3 conversion (f47ae615) · Commits · github_fork / Universc

launch_universc.sh

+13 −9

Original line number	Diff line number	Diff line
		@@ -1513,7 +1513,7 @@ fi
		#generate missing indexes if required (generating I1 and I2)
		if [[ "$technology" == "indrop-v3" ]] \|\| [[ "$technology" == "icell8-full-length" ]] \|\| [[ "$technology" == "sciseq2" ]] \|\| [[ "$technology" == "sciseq3" ]] \|\| [[ "$technology" == "scifiseq" ]] \|\| [[ "$technology" == "smartseq2" ]] \|\|[[ "$technology" == "smartseq3" ]] \|\| [[ "$technology" == "strt-seq-2i" ]] ; then
		echo "dual indexes I1 and I2 required for $technology"
		if [[ ${#index2[@]} -le 1 ]]; then
		if [[ ${#index2[@]} -le 0 ]]; then
		echo " automatically generating I1 and I2 index files from file headers"
		index1=("${read1[@]}")
		index2=("${read1[@]}")
		@@ -1545,7 +1545,7 @@ if [[ "$technology" == "indrop-v3" ]] \|\| [[ "$technology" == "icell8-full-lengt
		if [[ $verbose ]]; then
		echo index2 of length $index2length gives quality score $qualscores2
		fi
		sed -i "4~4s/^.*$/${qualscores2})/g" $I2_file
		sed -i "4~4s/^.*$/${qualscores2}/g" $I2_file
		index1+=("$I1_file")
		index2+=("$I2_file")
		done
		@@ -2026,7 +2026,7 @@ if [[ "$technology" != "10x" ]]; then
		fi
		if [[ "$technology" == "smartseq" ]] \|\| [[ "$technology" == "smartseq3" ]] \|\| [[ "$technology" == "icell8-5-prime" ]]; then
		if [[ $verbose ]]; then
		echo $chemistry
		echo " Using $chemistry for $technology"
		fi
		if [[ "$chemistry" == "fiveprime" ]]; then
		chemistry="SC5P-PE"
		@@ -3334,7 +3334,7 @@ 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=${convR1} --tag="ATTGCGCAATG" --out_dir=$crIN
		perl sub/ConcatenateDualIndexBarcodes.pl --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 ${convR1}
		@@ -3344,20 +3344,24 @@ else
		tsoS="TTTCTTATATGGG"
		tsoQ="IIIIIIIIIIIII"
		#Add 10x TSO characters to the end of the sequence
		cmd=$(echo 'sed -E "2~4s/(.{'$barcodelength'})(.{'${umilength}'})(.{3})/\1\2'$tsoS'/" '$convFile' > '${crIN}'/.temp')
		cmd=$(echo 'sed -E "2~4s/^(.{'$barcodelength'})(.{'${umilength}'})(.{'3'})/\1\2'$tsoS'/" '$convFile' > '${crIN}'/.temp')
		if [[ $verbose ]]; then
		echo technology $technology
		echo barcode: $barcodelength
		echo umi: $umilength
		echo $cmd
		fi
		# run command with barcode and umi length, e.g.,: sed -E "2~4s/(.{16})(.{8})(.{3})(.*)/\1\2$tsoS\4/" $convFile > ${crIN}/.temp
		# run command with barcode and umi length, e.g.,: sed -E "2~4s/^(.{16})(.{8})(.{'3'})(.*)/\1\2$tsoS\4/" $convFile > ${crIN}/.temp
		eval $cmd
		mv ${crIN}/.temp $convFile
		#Add n characters to the end of the quality
		cmd=$(echo 'sed -E "4~4s/(.{'$barcodelength'})(.{'${umilength}'})(.{3})/\1\2'$tsoQ'/" '$convFile' > '${crIN}'/.temp')
		# run command with barcode and umi length, e.g.,: sed -E "4~4s/(.{16})(.{8})(.{3})(.*)/\1\2$tsoQ\4/" $convFile > ${crIN}/.temp
		cmd=$(echo 'sed -E "4~4s/^(.{'$barcodelength'})(.{'${umilength}'})(.{'3'})/\1\2'$tsoQ'/" '$convFile' > '${crIN}'/.temp')
		# run command with barcode and umi length, e.g.,: sed -E "4~4s/^(.{16})(.{8})(.{'3'})(.*)/\1\2$tsoQ\4/" $convFile > ${crIN}/.temp
		if [[ $verbose ]]; then
		echo $cmd
		fi
		eval $cmd
		#returns an R file with the TSO replaced with the 13 bp 10x Genomics sequence
		mv ${crIN}/.temp $convFile
		echo " ${convFile} adjusted"
		done

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