Commit d6269f87 authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

add TSO with hardcoded barcode configuration for Smart-Seq3

parent ef4acd21
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+6 −3
Original line number Diff line number Diff line
@@ -2393,11 +2393,14 @@ else
            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 > ${crIN}/.temp
            # echo 'sed -E "4~4s/(.{$barcodelength})(.{$umilength})(.{3})/\1\2$tsoS/"  $convFile > ${crIN}/.temp'
            # sed -E "4~4s/(.{$barcodelength})(.{$umilength})(.{3})/\1\2$tsoS/"  $convFile > ${crIN}/.temp
            echo 'sed -E "2~4s/(.{16})(.{8})(.{3})(.*)/\1\2$tsoS\4/"  $convFile > ${crIN}/.temp'
            sed -E "2~4s/(.{16})(.{8})(.{3})(.*)/\1\2$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 > ${crIN}/.temp
            # sed -E "4~4s/(.{$barcodelength})(.{$umilength})(.{3})(.*)/\1\2$tsoQ\4/"  $convFile > ${crIN}/.temp
            sed -E "4~4s/(.{16})(.{8})(.{3})(.*)/\1\2$tsoQ\4/"  $convFile > ${crIN}/.temp
            mv ${crIN}/.temp $convFile
            echo "  ${convFile} adjusted"
        done