correct default chemistry for 5' with Smart-Seq (ef4acd21) · Commits · github_fork / Universc

launch_universc.sh

+28 −8

Original line number	Diff line number	Diff line
		@@ -619,7 +619,7 @@ elif [[ "$technology" == "scrbseq" ]] \|\| [[ "$technology" == "scrb-seq" ]] \|\| [[
		technology="scrbseq"
		elif [[ "$technology" == "seqwell" ]] \|\| [[ "$technology" == "seq-well" ]]; then
		technology="seqwell"
		elif [[ "$technology" == "smartseq" ]] \|\| [[ "$technology" == "smart-seq" ]] \|\| [[ "$technology" == "smartseq2" ]] \|\| [[ "$technology" == "smart-seq2" ]]
		elif [[ "$technology" == "smartseq" ]] \|\| [[ "$technology" == "smart-seq" ]] \|\| [[ "$technology" == "smartseq2" ]] \|\| [[ "$technology" == "smart-seq2" ]]; then
		technology="smartseq2"
		elif [[ "$technology" == "smartseq2-umi" ]] \|\| [[ "$technology" == "smart-seq2-umi" ]] \|\| [[ "$technology" == "smartseq3" ]] \|\| [[ "$technology" == "smart-seq3" ]]; then
		technology="smartseq"
		@@ -813,6 +813,7 @@ elif [[ "$chemistry" != "$temp_chemistry" ]]; then
		echo "*WARNING: chemistry is set to ${chemistry} where ${temp_chemistry} would have been chosen automatically. proceed with caution.*"
		fi


		#set default barcode and umi lengths
		barcode_default=16
		umi_default=10
		@@ -1609,10 +1610,13 @@ fi
		#allow "auto" only for 10x
		if [[ "$technology" != "10x" ]]; then
		#use SC3Pv3 (umi length 12)
		if [[ $umilength -ge 11 ]] && [[ "$chemistry" == "SC3Pv1" ]] && [[ "$chemistry" == "SC3Pv2" ]]; then
		if [[ $umilength -ge 11 ]]; then
		if [[ "$chemistry" == "SC3Pv1" ]] \|\| [[ "$chemistry" == "SC3Pv2" ]]; then
		echo "Using 10x version 3 chemistry to support longer UMIs"
		chemistry="SC3Pv3"
		else
		umi_default=12
		fi
		elif [[ "$chemistry" != "SC5P-PE" ]] && [[ "$chemistry" != "SC5P-R1" ]] && [[ "$chemistry" != "SC5P-R2" ]] && [[ "$chemistry" != "fiveprime" ]]; then
		#use SC3Pv2 (umi length 10)
		echo "Using 10x version 2 chemistry to support UMIs"
		chemistry="SC3Pv2"
		@@ -1623,10 +1627,13 @@ if [[ "$technology" != "10x" ]]; then
		fi
		fi
		if [[ "$technology" == "smartseq" ]] \|\| [[ "$technology" == "smartseq3" ]]; then
		if [[ $verbose ]]; then
		echo $chemistry
		fi
		if [[ "$chemistry" == "fiveprime" ]]; then
		chemistry="SC5P-PE"
		fi
		if [[ "$chemistry" != "SC5P-PE" ]] && [[ "$chemistry" != "SC5P-R2" ]] && [[ "$chemistry" != "SC5P-R2" ]]; then
		if [[ "$chemistry" != "SC5P-PE" ]] && [[ "$chemistry" != "SC5P-R1" ]] && [[ "$chemistry" != "SC5P-R2" ]]; then
		echo "Error: option --chemistry must be SC5P-PE, SC5P-R1 or SC5P-R2"
		exit
		fi
		@@ -2380,6 +2387,19 @@ else

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

		#convert TSO to expected length for 10x 5' (TSS in R1 from base 39)
		echo " handling $convFile ..."
		tsoS="TTTCTTATATGGG"
		tsoQ="IIIIIIIIIIIII"
		#Add 10x TSO characters to the end of the sequence
		sed -E "2~4s/(.{$barcodelength})(.{$umilength})(.{3})(.*)/\1\2$tsoS\4/" $convFile > ${crIN}/.temp
		mv ${crIN}/.temp $convFile
		#Add n characters to the end of the quality
		sed -E "4~4s/(.{$barcodelength})(.{$umilength})(.{3})(.*)/\1\2$tsoQ\4/" $convFile > ${crIN}/.temp
		sed -E "4~4s/(.{$keeplength})(.*)/\1$toQ\2/" $convFile > ${crIN}/.temp
		mv ${crIN}/.temp $convFile
		echo " ${convFile} adjusted"
		done
		fi
		#Smart-Seq2

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