Commit 791c1874 authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

update verbose output

parent 393cbaa1
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+2 −2
Original line number Diff line number Diff line
@@ -3343,7 +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 adapters 
            perl ${FILTERSMARTSEQREADUMI} --r1 ${convR1} --r2 ${convR2} --i1 ${convI1} --i2 ${convI2} --tag 'ATTGCGCAATG' --out_dir ${crIN}
            echo "  ...parsing reads with tag sequence and swoping 10x TSO for R1"
            echo "  ...parsing reads with tag sequence and replacing with 10x TSO for R1"
            
            # returns R1 with tag sequence removed (left trim) starting with 8pbp UMI and corresponding reads for I1, I2, and R2
            mv $crIN/parsed_R1.fastq ${convR1}