From dfe40fa941fa4a2f8f14d9ebf576baae2944dc0f Mon Sep 17 00:00:00 2001 From: Alexander Predeus Date: Mon, 17 Jan 2022 18:28:13 +0000 Subject: [PATCH] QC script update --- scripts/solo_QC.sh | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/scripts/solo_QC.sh b/scripts/solo_QC.sh index 6d5c80f..1cdcb35 100755 --- a/scripts/solo_QC.sh +++ b/scripts/solo_QC.sh @@ -1,6 +1,6 @@ #!/bin/bash -echo -e "Sample\tRd_all\tRd_in_cells\tUMI_in_cells\tCells\tMed_nFeature\tGood_BC\tall_u+m\tall_u\texon_u+m\texon_u\tfull_u+m\tfull_u" +echo -e "Sample\tRd_all\tRd_in_cells\tFrc_in_cells\tUMI_in_cells\tCells\tMed_nFeature\tGood_BC\tall_u+m\tall_u\texon_u+m\texon_u\tfull_u+m\tfull_u" for i in * do @@ -16,8 +16,9 @@ do F2=`grep "Reads Mapped to GeneFull: Unique GeneFull," $i/output/GeneFull/Summary.csv | awk -F "," '{print $2}'` C=`grep "Estimated Number of Cells," $i/output/GeneFull/Summary.csv | awk -F "," '{print $2}'` R2=`grep "Unique Reads in Cells Mapped to GeneFull," $i/output/GeneFull/Summary.csv | awk -F "," '{print $2}'` + CF=`echo $R1 | awk -v v=$R2 '{printf "%.3f\n",v/$1}'` R3=`grep "UMIs in Cells," $i/output/GeneFull/Summary.csv | awk -F "," '{print $2}'` GC=`grep "Median GeneFull per Cell," $i/output/GeneFull/Summary.csv | awk -F "," '{print $2}'` - echo -e "$i\t$R1\t$R2\t$R3\t$C\t$GC\t$B\t$G1\t$G2\t$T1\t$T2\t$F1\t$F2" + echo -e "$i\t$R1\t$R2\t$CF\t$R3\t$C\t$GC\t$B\t$G1\t$G2\t$T1\t$T2\t$F1\t$F2" fi done