Commit 5245ab97 authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

update HEK293T test data for SmartSeq3

parent 4920e6cd

test/run_tests_smartseq3_gh_actions.sh

+2 −2
Original line number Diff line number Diff line
@@ -42,7 +42,7 @@ fi 
# call on smartseq3 with files

bash launch_universc.sh --id "test-smartseq3" --technology "smartseq3" \

 --reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \

 --read1 "test/shared/smartseq3-test/Smartseq3_diySpike_R1" \

 --read2 "test/shared/smartseq3-test/Smartseq3_diySpike_R2" \

 --read1 "test/shared/smartseq3-test/test-smartseq-hek293t_S2_L001_R1" \

 --read2 "test/shared/smartseq3-test/test-smartseq-hek293t_S2_L001_R2" \

 --barcodefile "${whitelistdir}/test_bcs_small.txt" \

 --jobmode "local" --localcores 1

test/run_tests_smartseq3_local.sh

+18 −238
Original line number Diff line number Diff line
@@ -21,32 +21,19 @@ if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA ]] && [[ 
    rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA

fi



# compress all input files

if [[ -f test/shared/smartseq3-test/Smartseq3.Fibroblasts.GelCut.R1.fastq ]]; then

echo    gzip test/shared/smartseq3-test//Smartseq3.Fibroblasts.GelCut*fastq

fi



#mv  test/shared/smartseq3-test/Smartseq3.Fibroblasts.GelCut.L001_R1_001.fastq.gz  test/shared/smartseq3-test/Smartseq3.Fibroblasts.GelCut.R1.fastq.gz

#mv  test/shared/smartseq3-test/Smartseq3.Fibroblasts.GelCut.L001_R2_001.fastq.gz  test/shared/smartseq3-test/Smartseq3.Fibroblasts.GelCut.R2.fastq.gz

#mv  test/shared/smartseq3-test/Smartseq3.Fibroblasts.GelCut.L001_I1_001.fastq.gz  test/shared/smartseq3-test/Smartseq3.Fibroblasts.GelCut.I1.fastq.gz

#mv  test/shared/smartseq3-test/Smartseq3.Fibroblasts.GelCut.L001_I2_001.fastq.gz  test/shared/smartseq3-test/Smartseq3.Fibroblasts.GelCut.I2.fastq.gz



rename -f "s/_S1_L001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_S1_L001_[IR][12]_001.fastq

rename -f "s/_001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_[IR][12]_001.fastq



#rename "s/Smartseq3.Fibroblasts.GelCut./Smartseq3_Fibroblasts_GelCut_/g"  test/shared/smartseq3-test/Smartseq3.Fibroblasts.GelCut.[IR][12].fastq

#rename "s/Smartseq3.Fibroblasts.GelCut./Smartseq3_Fibroblasts_GelCut_/g"  test/shared/smartseq3-test/Smartseq3.Fibroblasts.GelCut.L001.[IR][12].fastq

while [[ ! -f /home/tom/repos/universc/test-10x-hek293t/outs/metrics_summary.csv  ]]; do

    echo "wait ..."

    sleep 60

done



# test manual setup

bash launch_universc.sh -t "smartseq3" --setup --barcodefile "whitelists/test_bcs_small.txt"



if [[ false ]]; then



if [[ -d input4cellranger_test-smartseq3-gelcut-small-hard ]]; then

    rm -rf input4cellranger_test-smartseq3-gelcut-small-hard

if [[ -d input4cellranger_test-smartseq3-hek293t-test-chr21 ]]; then

    rm -rf input4cellranger_test-smartseq3-hek293t-test-chr21

fi

if [[ -d test-smartseq3-gelcut-small-hard ]]; then

    rm -rf test-smartseq3-gelcut-small-hard

if [[ -d test-smartseq3-hek293t-test-chr21 ]]; then

    rm -rf test-smartseq3-hek293t-test-chr21

fi



if [[ ! -f whitelists/SmartSeq3_test_barcodes.txt ]]; then
@@ -54,227 +41,20 @@ if [[ ! -f whitelists/SmartSeq3_test_barcodes.txt ]]; then 
fi





skip="false"

#while [[ ! -f /home/tom/repos/universc/test-smartseq3-gelcut/outs/metrics_summary.csv  ]]; do

#    echo "wait ..."

#    sleep 60

#done



#gzip -fk test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_[IR][12].fastq



 # call on smartseq3 with files

bash launch_universc.sh --id "test-smartseq3-gelcut-small-hard-5pr2-hg38" --technology "smartseq3" \

 --chemistry "SC5P-R2" \

 --reference "~/reference/cellranger/refdata-cellranger-GRCh38-3.0.0" \

 --read1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_R1.fastq" \

 --read2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_R2.fastq" \

 --index1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_I1.fastq" \

 --index2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_I2.fastq" \

 --barcodefile "whitelists/Smartseq3_Fibroblasts_GelCut_small_bcs.txt" \

 --per-cell-data --jobmode "sge" --verbose #--as-is # "local" --localcores 1



if [ -f test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_S1_L001_R1_001.fastq ]; then

    rename "s/_S1_L001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_S1_L001_[IR][12]_001.fastq*

    rename "s/_001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_[IR][12]_001.fastq*

fi



fi



 # call on smartseq3 with files

bash launch_universc.sh --id "test-smartseq3-gelcut-small-hard-5pr1-hg38" --technology "smartseq3" \

 --chemistry "SC5P-R1" \

 --reference "~/reference/cellranger/refdata-cellranger-GRCh38-3.0.0" \

 --read1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_R1.fastq" \

 --read2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_R2.fastq" \

 --index1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_I1.fastq" \

 --index2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_I2.fastq" \

 --barcodefile "whitelists/Smartseq3_Fibroblasts_GelCut_small_bcs.txt" \

 --per-cell-data --jobmode "sge" --verbose #--as-is # "local" --localcores 1



if [ -f test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_S1_L001_R1_001.fastq ]; then

    rename "s/_S1_L001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_S1_L001_[IR][12]_001.fastq*

    rename "s/_001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_[IR][12]_001.fastq*

fi

#gzip -fk test/shared/smartseq3-test/Smartseq3_diySpike_[IR][12].fastq



 # call on smartseq3 with files

bash launch_universc.sh --id "test-smartseq3-gelcut-small-hard-hg38" --technology "smartseq3" \

bash launch_universc.sh --id "test-smartseq3-hek293t-test-chr21" --technology "smartseq3" \

 --chemistry "SC5P-PE" \

 --reference "~/reference/cellranger/refdata-cellranger-GRCh38-3.0.0" \

 --read1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_R1.fastq" \

 --read2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_R2.fastq" \

 --index1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_I1.fastq" \

 --index2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_I2.fastq" \

 --barcodefile "whitelists/Smartseq3_Fibroblasts_GelCut_small_bcs.txt" \

 --per-cell-data --jobmode "sge" --verbose #--as-is # "local" --localcores 1



if [ -f test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_S1_L001_R1_001.fastq ]; then

    rename "s/_S1_L001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_S1_L001_[IR][12]_001.fastq*

    rename "s/_001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_[IR][12]_001.fastq*

fi



 # call on smartseq3 with files

bash launch_universc.sh --id "test-smartseq3-gelcut-small-hard-5pr2" --technology "smartseq3" \

 --chemistry "SC5P-R2" \

 --reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \

 --read1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_R1.fastq" \

 --read2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_R2.fastq" \

 --index1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_I1.fastq" \

 --index2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_I2.fastq" \

 --barcodefile "whitelists/Smartseq3_Fibroblasts_GelCut_small_bcs.txt" \

 --per-cell-data --jobmode "sge" --verbose #--as-is # "local" --localcores 1



if [ -f test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_S1_L001_R1_001.fastq ]; then

    rename "s/_S1_L001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_S1_L001_[IR][12]_001.fastq*

    rename "s/_001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_[IR][12]_001.fastq*

fi



 # call on smartseq3 with files

bash launch_universc.sh --id "test-smartseq3-gelcut-small-hard-5pr1" --technology "smartseq3" \

 --chemistry "SC5P-R1" \

 --reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \

 --read1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_R1.fastq" \

 --read2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_R2.fastq" \

 --index1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_I1.fastq" \

 --index2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_I2.fastq" \

 --barcodefile "whitelists/Smartseq3_Fibroblasts_GelCut_small_bcs.txt" \

 --read1 "test/shared/smartseq3-test/test-smartseq-hek293t_S2_L001_R1_001.fastq.gz" \

 --read2 "test/shared/smartseq3-test/test-smartseq-hek293t_S2_L001_R2_001.fastq.gz" \

 --index1 "test/shared/smartseq3-test/test-smartseq-hek293t_S2_L001_I1_001.fastq.gz" \

 --index2 "test/shared/smartseq3-test/test-smartseq-hek293t_S2_L001_I2_001.fastq.gz" \

 --barcodefile "whitelists/Smartseq3_diySpike_small_bcs.txt" \

 --per-cell-data --jobmode "sge" --verbose #--as-is # "local" --localcores 1



if [ -f test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_S1_L001_R1_001.fastq ]; then

    rename "s/_S1_L001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_S1_L001_[IR][12]_001.fastq*

    rename "s/_001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_[IR][12]_001.fastq*

fi



 # call on smartseq3 with files

bash launch_universc.sh --id "test-smartseq3-gelcut-small-hard" --technology "smartseq3" \

 --chemistry "SC5P-PE" \

 --reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \

 --read1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_R1.fastq" \

 --read2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_R2.fastq" \

 --index1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_I1.fastq" \

 --index2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_I2.fastq" \

 --barcodefile "whitelists/Smartseq3_Fibroblasts_GelCut_small_bcs.txt" \

 --per-cell-data --jobmode "sge" --verbose #--as-is # "local" --localcores 1



if [ -f test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_S1_L001_R1_001.fastq ]; then

    rename "s/_S1_L001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_S1_L001_[IR][12]_001.fastq*

    rename "s/_001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_[IR][12]_001.fastq*

fi



#exit 0



if [[ -d input4cellranger_test-smartseq3-gelcut-small ]]; then

    rm -rf input4cellranger_test-smartseq3-gelcut-small

if [ -f test/shared/smartseq3-test/test-smartseq-hek293t_S2_L001_R1_001.fastq ]; then

    rename "s/_S1_L001//" test/shared/smartseq3-test/test-smartseq-hek293t_S2_L001_[IR][12]_001.fastq*

    rename "s/_001//" test/shared/smartseq3-test/Smartseq3_diySpike_[IR][12]_001.fastq*

fi
 
if [[ -d test-smartseq3-gelcut-small ]]; then

    rm -rf test-smartseq3-gelcut-small

fi





# call on smartseq3 with files

bash launch_universc.sh --id "test-smartseq3-gelcut-small-5pr2-hg38" --technology "smartseq3" \

 --chemistry "SC5P-R2" \

 --reference "~/reference/cellranger/refdata-cellranger-GRCh38-3.0.0" \

 --read1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_R1.fastq" \

 --read2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_R2.fastq" \

 --index1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_I1.fastq" \

 --index2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_I2.fastq" \

 --barcodefile "whitelists/Smartseq3_Fibroblasts_GelCut_small_bcs.txt" \

 --per-cell-data --jobmode "sge" #--as-is # "local" --localcores 1



# --barcodefile "whitelists/SmartSeq3_test_barcodes.txt" \



if [ -f test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_S1_L001_R1_001.fastq ]; then

    rename "s/_S1_L001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_S1_L001_[IR][12]_001.fastq*

    rename "s/_001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_[IR][12]_001.fastq*

fi



# call on smartseq3 with files

bash launch_universc.sh --id "test-smartseq3-gelcut-small-5pr1-hg38" --technology "smartseq3" \

 --chemistry "SC5P-R1" \

 --reference "~/reference/cellranger/refdata-cellranger-GRCh38-3.0.0" \

 --read1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_R1.fastq" \

 --read2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_R2.fastq" \

 --index1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_I1.fastq" \

 --index2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_I2.fastq" \

 --barcodefile "whitelists/Smartseq3_Fibroblasts_GelCut_small_bcs.txt" \

 --per-cell-data --jobmode "sge" #--as-is # "local" --localcores 1



# --barcodefile "whitelists/SmartSeq3_test_barcodes.txt" \



if [ -f test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_S1_L001_R1_001.fastq ]; then

    rename "s/_S1_L001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_S1_L001_[IR][12]_001.fastq*

    rename "s/_001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_[IR][12]_001.fastq*

fi



# call on smartseq3 with files

bash launch_universc.sh --id "test-smartseq3-gelcut-small-hg38" --technology "smartseq3" \

 --chemistry "SC5P-PE" \

 --reference "~/reference/cellranger/refdata-cellranger-GRCh38-3.0.0" \

 --read1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_R1.fastq" \

 --read2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_R2.fastq" \

 --index1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_I1.fastq" \

 --index2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_I2.fastq" \

 --barcodefile "whitelists/Smartseq3_Fibroblasts_GelCut_small_bcs.txt" \

 --per-cell-data --jobmode "sge" #--as-is # "local" --localcores 1



# --barcodefile "whitelists/SmartSeq3_test_barcodes.txt" \



if [ -f test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_S1_L001_R1_001.fastq ]; then

    rename "s/_S1_L001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_S1_L001_[IR][12]_001.fastq*

    rename "s/_001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_[IR][12]_001.fastq*

fi



# call on smartseq3 with files

bash launch_universc.sh --id "test-smartseq3-gelcut-small-5pr2" --technology "smartseq3" \

 --chemistry "SC5P-R2" \

 --reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \

 --read1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_R1.fastq" \

 --read2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_R2.fastq" \

 --index1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_I1.fastq" \

 --index2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_I2.fastq" \

 --barcodefile "whitelists/Smartseq3_Fibroblasts_GelCut_small_bcs.txt" \

 --per-cell-data --jobmode "sge" #--as-is # "local" --localcores 1



# --barcodefile "whitelists/SmartSeq3_test_barcodes.txt" \



if [ -f test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_S1_L001_R1_001.fastq ]; then

    rename "s/_S1_L001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_S1_L001_[IR][12]_001.fastq*

    rename "s/_001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_[IR][12]_001.fastq*

fi



# call on smartseq3 with files

bash launch_universc.sh --id "test-smartseq3-gelcut-small-5pr1" --technology "smartseq3" \

 --chemistry "SC5P-R1" \

 --reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \

 --read1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_R1.fastq" \

 --read2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_R2.fastq" \

 --index1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_I1.fastq" \

 --index2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_I2.fastq" \

 --barcodefile "whitelists/Smartseq3_Fibroblasts_GelCut_small_bcs.txt" \

 --per-cell-data --jobmode "sge" #--as-is # "local" --localcores 1



# --barcodefile "whitelists/SmartSeq3_test_barcodes.txt" \



if [ -f test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_S1_L001_R1_001.fastq ]; then

    rename "s/_S1_L001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_S1_L001_[IR][12]_001.fastq*

    rename "s/_001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_[IR][12]_001.fastq*

fi



# call on smartseq3 with files

bash launch_universc.sh --id "test-smartseq3-gelcut-small" --technology "smartseq3" \

 --chemistry "SC5P-PE" \

 --reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \

 --read1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_R1.fastq" \

 --read2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_R2.fastq" \

 --index1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_I1.fastq" \

 --index2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_I2.fastq" \

 --barcodefile "whitelists/Smartseq3_Fibroblasts_GelCut_small_bcs.txt" \

 --per-cell-data --jobmode "sge" #--as-is # "local" --localcores 1



# --barcodefile "whitelists/SmartSeq3_test_barcodes.txt" \



if [ -f test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_S1_L001_R1_001.fastq ]; then

    rename "s/_S1_L001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_S1_L001_[IR][12]_001.fastq*

    rename "s/_001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_[IR][12]_001.fastq*

fi

test/run_tests_smartseq3_local_diyspike.sh

0 → 100755
+68 −0
Original line number Diff line number Diff line 


#!/bin/bash

bash ~/.bashrc



# run tests in universc directory (parent of test directory)

cd $(dirname ${BASH_SOURCE[0]})/..

pwd

##git pull --ff-only origin $(git branch --show-current) 



# used to export to PATH for testing on SGE server

export PATH=${HOME}/local/bin/cellranger-3.0.2:$PATH



cellrangerversion=`cellranger count --version | head -n 2 | tail -n 1 | cut -f2 -d'(' | cut -f1 -d')'`

cellrangerpath=`which cellranger`



# set up cellranger reference

if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA ]]; then

    rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA

fi

if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA ]]; then

    rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA

fi



# compress all input files

if [[ -f test/shared/smartseq3-test/Smartseq3.diySpike.R1.fastq ]]; then

echo    gzip test/shared/smartseq3-test//Smartseq3.diySpike*fastq

fi



rename -f "s/_S1_L001//" test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_[IR][12]_001.fastq

rename -f "s/_001//" test/shared/smartseq3-test/Smartseq3_diySpike_[IR][12]_001.fastq



#rename "s/Smartseq3.diySpike./Smartseq3_diySpike_/g"  test/shared/smartseq3-test/Smartseq3.diySpike.[IR][12].fastq

#rename "s/Smartseq3.diySpike./Smartseq3_diySpike_/g"  test/shared/smartseq3-test/Smartseq3.diySpike.L001.[IR][12].fastq



while [[ ! -f /home/tom/repos/universc/test-10x-hek293t/outs/metrics_summary.csv  ]]; do

    echo "wait ..."

    sleep 60

done



# test manual setup

bash launch_universc.sh -t "smartseq3" --setup --barcodefile "whitelists/test_bcs_small.txt"



if [[ -d input4cellranger_test-smartseq3-diyspike-hg38 ]]; then

    rm -rf input4cellranger_test-smartseq3-diyspike-hg38

fi

if [[ -d test-smartseq3-diyspike-hg38 ]]; then

    rm -rf test-smartseq3-diyspike-hg38

fi



if [[ ! -f whitelists/SmartSeq3_test_barcodes.txt ]]; then

    gunzip -k whitelists/SmartSeq3_test_barcodes.txt.gz

fi



 # call on smartseq3 with files

bash launch_universc.sh --id "test-smartseq3-diyspike-hg38" --technology "smartseq3" \

 --chemistry "SC5P-PE" \

 --reference "~/reference/cellranger/refdata-cellranger-GRCh38-3.0.0" \

 --read1 "test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R1_001.fastq.gz" \

 --read2 "test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R2_001.fastq" \

 --index1 "test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_I1_001.fastq" \

 --index2 "test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_I2_001.fastq" \

 --barcodefile "whitelists/Smartseq3_diySpike_small_bcs.txt" \

 --per-cell-data --jobmode "sge" --verbose #--as-is # "local" --localcores 1



if [ -f test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R1_001.fastq ]; then

    rename "s/_S1_L001//" test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_[IR][12]_001.fastq*

    rename "s/_001//" test/shared/smartseq3-test/Smartseq3_diySpike_[IR][12]_001.fastq*

fi

test/shared/smartseq3-test/prepare_files.sh

+19 −19
Original line number Diff line number Diff line
@@ -8,31 +8,31 @@ rename "s/.diySpike./_diySpike_S1_L001_/g" *gz 


#create bowtie index

bowtie2-build ../../test/cellranger_reference/cellranger-tiny-ref/3.0.0/fasta/genome.fa ../../test/cellranger_reference/cellranger-tiny-ref/3.0.0/fasta/genome

bowtie2 -x ../../test/cellranger_reference/cellranger-tiny-ref/3.0.0/fasta/genome -U Smartseq3_diySpike_S1_L001_R2_001.001.fastq -S Smartseq3_diySpike_S1_L001_R2_001.001.sam

samtools view -bS Smartseq3_diySpike_S1_L001_R2_001.001.sam > Smartseq3_diySpike_S1_L001_R2_001.001.bam

bowtie2 -x ../../test/cellranger_reference/cellranger-tiny-ref/3.0.0/fasta/genome -U Smartseq3_diySpike_S1_L001_R2_001.fastq -S Smartseq3_diySpike_S1_L001_R2_001.sam

samtools view -bS Smartseq3_diySpike_S1_L001_R2_001.sam > Smartseq3_diySpike_S1_L001_R2_001.bam



# extract region of genome

samtools sort -O BAM Smartseq3_diySpike_S1_L001_R2_001.001.bam > Smartseq3_diySpike_S1_L001_R2_001.001.sort.bam

samtools index Smartseq3_diySpike_S1_L001_R2_001.001.sort.bam

samtools view  Smartseq3_diySpike_S1_L001_R2_001.001.sort.bam  21:9825832-48085036 > Smartseq3_diySpike_S1_L001_R2_001.001.chr21.bam

samtools view -O BAM  Smartseq3_diySpike_S1_L001_R2_001.001.sort.bam  21:9825832-48085036 > Smartseq3_diySpike_S1_L001_R2_001.001.chr21.sort.bam

samtools sort -n Smartseq3_diySpike_S1_L001_R2_001.001.chr21.sort.bam -o Smartseq3_diySpike_S1_L001_R2_001.001.chr21.qsort.bam

samtools sort -O BAM Smartseq3_diySpike_S1_L001_R2_001.bam > Smartseq3_diySpike_S1_L001_R2_001.sort.bam

samtools index Smartseq3_diySpike_S1_L001_R2_001.sort.bam

samtools view  Smartseq3_diySpike_S1_L001_R2_001.sort.bam  21:9825832-48085036 > Smartseq3_diySpike_S1_L001_R2_001.chr21.bam

samtools view -O BAM  Smartseq3_diySpike_S1_L001_R2_001.sort.bam  21:9825832-48085036 > Smartseq3_diySpike_S1_L001_R2_001.chr21.sort.bam

samtools sort -n Smartseq3_diySpike_S1_L001_R2_001.chr21.sort.bam -o Smartseq3_diySpike_S1_L001_R2_001.chr21.qsort.bam



# export mapped regions to fastq

bedtools bamtofastq -i Smartseq3_diySpike_S1_L001_R2_001.001.chr21.qsort.bam -fq Smartseq3_diySpike_S1_L001_R2_001.001.chr21_R2.fastq

fastq_pair Smartseq3_diySpike_S1_L001_R2_001.001.chr21_R2.fastq Smartseq3_diySpike_S1_L001_R1_001.fastq

fastq_pair Smartseq3_diySpike_S1_L001_R2_001.001.chr21_R2.fastq Smartseq3_diySpike_S1_L001_I1_001.001.fastq

fastq_pair Smartseq3_diySpike_S1_L001_R2_001.001.chr21_R2.fastq Smartseq3_diySpike_S1_L001_I2_001.001.fastq

bedtools bamtofastq -i Smartseq3_diySpike_S1_L001_R2_001.chr21.qsort.bam -fq Smartseq3_diySpike_S1_L001_R2_001.chr21_R2.fastq

fastq_pair Smartseq3_diySpike_S1_L001_R2_001.chr21_R2.fastq Smartseq3_diySpike_S1_L001_R1_001.fastq

fastq_pair Smartseq3_diySpike_S1_L001_R2_001.chr21_R2.fastq Smartseq3_diySpike_S1_L001_I1_001.fastq

fastq_pair Smartseq3_diySpike_S1_L001_R2_001.chr21_R2.fastq Smartseq3_diySpike_S1_L001_I2_001.fastq



# downsample to 250,000 reads per "lane"

seqtk sample -s999 Smartseq3_diySpike_S1_L001_R1_001.fastq.paired.fq 250000 > Smartseq3_diySpike_S1_L001_L001_R1_001.fastq

seqtk sample -s999 Smartseq3_diySpike_S1_L001_R2_001.001.chr21_R2.fastq.paired.fq 250000 > Smartseq3_diySpike_S1_L001_L001_R2_001.001.fastq

seqtk sample -s999 Smartseq3_diySpike_S1_L001_I1_001.001.fastq.paired.fq 250000 > Smartseq3_diySpike_S1_L001_L001_I1_001.001.fastq

seqtk sample -s999 Smartseq3_diySpike_S1_L001_I2_001.001.fastq.paired.fq 250000 > Smartseq3_diySpike_S1_L001_L001_I2_001.001.fastq

seqtk sample -s100 Smartseq3_diySpike_S1_L001_R1_001.fastq.paired.fq 250000 > Smartseq3_diySpike_S1_L001_L002_R1_001.fastq

seqtk sample -s100 Smartseq3_diySpike_S1_L001_R2_001.001.chr21_R2.fastq.paired.fq 250000 > Smartseq3_diySpike_S1_L001_L002_R2_001.fastq

seqtk sample -s100 Smartseq3_diySpike_S1_L001_I1_001.001.fastq.paired.fq 250000 > Smartseq3_diySpike_S1_L001_L001_I1_001.001.fastq

seqtk sample -s100 Smartseq3_diySpike_S1_L001_I2_001.001.fastq.paired.fq 250000 > Smartseq3_diySpike_S1_L001_L001_I2_001.001.fastq

seqtk sample -s999 Smartseq3_diySpike_S1_L001_R1_001.fastq.paired.fq 250000 > test-smartseq-hek293t_S2_L001_R1_001.fastq

seqtk sample -s999 Smartseq3_diySpike_S1_L001_R2_001.chr21_R2.fastq.paired.fq 250000 > test-smartseq-hek293t_S2_L001_R2_001.fastq

seqtk sample -s999 Smartseq3_diySpike_S1_L001_I1_001.fastq.paired.fq 250000 > test-smartseq-hek293t_S2_L001_I1_001.fastq

seqtk sample -s999 Smartseq3_diySpike_S1_L001_I2_001.fastq.paired.fq 250000 > test-smartseq-hek293t_S2_L001_I2_001.fastq

seqtk sample -s100 Smartseq3_diySpike_S1_L001_R1_001.fastq.paired.fq 250000 > test-smartseq-hek293t_S2_L002_R1_001.fastq

seqtk sample -s100 Smartseq3_diySpike_S1_L001_R2_001.chr21_R2.fastq.paired.fq 250000 > test-smartseq-hek293t_S2_L002_R2_001.fastq

seqtk sample -s100 Smartseq3_diySpike_S1_L001_I1_001.fastq.paired.fq 250000 > test-smartseq-hek293t_S2_L002_I1_001.fastq

seqtk sample -s100 Smartseq3_diySpike_S1_L001_I2_001.fastq.paired.fq 250000 > test-smartseq-hek293t_S2_L002_I2_001.fastq



#subsample smaller files for testing

rename "s/Smartseq3_diySpike_S1_L001_/Smartseq3_diySpike_S1_L001_/g" Smartseq3_diySpike_S1_L001_*fastq*

test/shared/smartseq3-test/test-smartseq-hek293t_S2_L001_I1_001.fastq.gz

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+132 B

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