Sample	command
10x-Genomics-Libraries-Geo10x5-A3-MultipleA_S10_L001	/gscratch/srlab/programs/fastp-0.20.0/fastp --in1 10x-Genomics-Libraries-Geo10x5-A3-MultipleA_S10_L001_R1_001.fastq.gz --in2 10x-Genomics-Libraries-Geo10x5-A3-MultipleA_S10_L001_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html 10x-Genomics-Libraries-Geo10x5-A3-MultipleA_S10_L001}.fastp-trim.20210401.report.html --json 10x-Genomics-Libraries-Geo10x5-A3-MultipleA_S10_L001.fastp-trim.20210401.report.json --out1 10x-Genomics-Libraries-Geo10x5-A3-MultipleA_S10_L001_R1_001.fastp-trim.20210401.fq.gz --out2 10x-Genomics-Libraries-Geo10x5-A3-MultipleA_S10_L001_R2_001.fastp-trim.20210401.fq.gz 
10x-Genomics-Libraries-Geo10x5-A3-MultipleA_S10_L002	/gscratch/srlab/programs/fastp-0.20.0/fastp --in1 10x-Genomics-Libraries-Geo10x5-A3-MultipleA_S10_L002_R1_001.fastq.gz --in2 10x-Genomics-Libraries-Geo10x5-A3-MultipleA_S10_L002_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html 10x-Genomics-Libraries-Geo10x5-A3-MultipleA_S10_L002}.fastp-trim.20210401.report.html --json 10x-Genomics-Libraries-Geo10x5-A3-MultipleA_S10_L002.fastp-trim.20210401.report.json --out1 10x-Genomics-Libraries-Geo10x5-A3-MultipleA_S10_L002_R1_001.fastp-trim.20210401.fq.gz --out2 10x-Genomics-Libraries-Geo10x5-A3-MultipleA_S10_L002_R2_001.fastp-trim.20210401.fq.gz 
10x-Genomics-Libraries-Geo10x5-A3-MultipleA_S10_L002_R1_001	/gscratch/srlab/programs/fastp-0.20.0/fastp --in1 10x-Genomics-Libraries-Geo10x5-A3-MultipleA_S10_L002_R1_001.fastq.gz --in2 10x-Genomics-Libraries-Geo10x5-A3-MultipleA_S10_L002_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html 10x-Genomics-Libraries-Geo10x5-A3-MultipleA_S10_L002_R1_001.fastp-trim.20210401.report.html --json 10x-Genomics-Libraries-Geo10x5-A3-MultipleA_S10_L002_R1_001.fastp-trim.20210401.report.json --out1 10x-Genomics-Libraries-Geo10x5-A3-MultipleA_S10_L002_R1_001.fastp-trim.20210401.fq.gz --out2 10x-Genomics-Libraries-Geo10x5-A3-MultipleA_S10_L002_R2_001.fastp-trim.20210401.fq.gz 
10x-Genomics-Libraries-Geo10x5-A3-MultipleB_S11_L001	/gscratch/srlab/programs/fastp-0.20.0/fastp --in1 10x-Genomics-Libraries-Geo10x5-A3-MultipleB_S11_L001_R1_001.fastq.gz --in2 10x-Genomics-Libraries-Geo10x5-A3-MultipleB_S11_L001_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html 10x-Genomics-Libraries-Geo10x5-A3-MultipleB_S11_L001}.fastp-trim.20210401.report.html --json 10x-Genomics-Libraries-Geo10x5-A3-MultipleB_S11_L001.fastp-trim.20210401.report.json --out1 10x-Genomics-Libraries-Geo10x5-A3-MultipleB_S11_L001_R1_001.fastp-trim.20210401.fq.gz --out2 10x-Genomics-Libraries-Geo10x5-A3-MultipleB_S11_L001_R2_001.fastp-trim.20210401.fq.gz 
10x-Genomics-Libraries-Geo10x5-A3-MultipleB_S11_L002	/gscratch/srlab/programs/fastp-0.20.0/fastp --in1 10x-Genomics-Libraries-Geo10x5-A3-MultipleB_S11_L002_R1_001.fastq.gz --in2 10x-Genomics-Libraries-Geo10x5-A3-MultipleB_S11_L002_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html 10x-Genomics-Libraries-Geo10x5-A3-MultipleB_S11_L002}.fastp-trim.20210401.report.html --json 10x-Genomics-Libraries-Geo10x5-A3-MultipleB_S11_L002.fastp-trim.20210401.report.json --out1 10x-Genomics-Libraries-Geo10x5-A3-MultipleB_S11_L002_R1_001.fastp-trim.20210401.fq.gz --out2 10x-Genomics-Libraries-Geo10x5-A3-MultipleB_S11_L002_R2_001.fastp-trim.20210401.fq.gz 
10x-Genomics-Libraries-Geo10x5-A3-MultipleC_S12_L001	/gscratch/srlab/programs/fastp-0.20.0/fastp --in1 10x-Genomics-Libraries-Geo10x5-A3-MultipleC_S12_L001_R1_001.fastq.gz --in2 10x-Genomics-Libraries-Geo10x5-A3-MultipleC_S12_L001_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html 10x-Genomics-Libraries-Geo10x5-A3-MultipleC_S12_L001}.fastp-trim.20210401.report.html --json 10x-Genomics-Libraries-Geo10x5-A3-MultipleC_S12_L001.fastp-trim.20210401.report.json --out1 10x-Genomics-Libraries-Geo10x5-A3-MultipleC_S12_L001_R1_001.fastp-trim.20210401.fq.gz --out2 10x-Genomics-Libraries-Geo10x5-A3-MultipleC_S12_L001_R2_001.fastp-trim.20210401.fq.gz 
10x-Genomics-Libraries-Geo10x5-A3-MultipleC_S12_L002	/gscratch/srlab/programs/fastp-0.20.0/fastp --in1 10x-Genomics-Libraries-Geo10x5-A3-MultipleC_S12_L002_R1_001.fastq.gz --in2 10x-Genomics-Libraries-Geo10x5-A3-MultipleC_S12_L002_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html 10x-Genomics-Libraries-Geo10x5-A3-MultipleC_S12_L002}.fastp-trim.20210401.report.html --json 10x-Genomics-Libraries-Geo10x5-A3-MultipleC_S12_L002.fastp-trim.20210401.report.json --out1 10x-Genomics-Libraries-Geo10x5-A3-MultipleC_S12_L002_R1_001.fastp-trim.20210401.fq.gz --out2 10x-Genomics-Libraries-Geo10x5-A3-MultipleC_S12_L002_R2_001.fastp-trim.20210401.fq.gz 
10x-Genomics-Libraries-Geo10x5-A3-MultipleD_S13_L001	/gscratch/srlab/programs/fastp-0.20.0/fastp --in1 10x-Genomics-Libraries-Geo10x5-A3-MultipleD_S13_L001_R1_001.fastq.gz --in2 10x-Genomics-Libraries-Geo10x5-A3-MultipleD_S13_L001_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html 10x-Genomics-Libraries-Geo10x5-A3-MultipleD_S13_L001}.fastp-trim.20210401.report.html --json 10x-Genomics-Libraries-Geo10x5-A3-MultipleD_S13_L001.fastp-trim.20210401.report.json --out1 10x-Genomics-Libraries-Geo10x5-A3-MultipleD_S13_L001_R1_001.fastp-trim.20210401.fq.gz --out2 10x-Genomics-Libraries-Geo10x5-A3-MultipleD_S13_L001_R2_001.fastp-trim.20210401.fq.gz 
10x-Genomics-Libraries-Geo10x5-A3-MultipleD_S13_L002	/gscratch/srlab/programs/fastp-0.20.0/fastp --in1 10x-Genomics-Libraries-Geo10x5-A3-MultipleD_S13_L002_R1_001.fastq.gz --in2 10x-Genomics-Libraries-Geo10x5-A3-MultipleD_S13_L002_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html 10x-Genomics-Libraries-Geo10x5-A3-MultipleD_S13_L002}.fastp-trim.20210401.report.html --json 10x-Genomics-Libraries-Geo10x5-A3-MultipleD_S13_L002.fastp-trim.20210401.report.json --out1 10x-Genomics-Libraries-Geo10x5-A3-MultipleD_S13_L002_R1_001.fastp-trim.20210401.fq.gz --out2 10x-Genomics-Libraries-Geo10x5-A3-MultipleD_S13_L002_R2_001.fastp-trim.20210401.fq.gz 
10x-Genomics-Libraries-Geo10x6-B3-MultipleA_S14_L001	/gscratch/srlab/programs/fastp-0.20.0/fastp --in1 10x-Genomics-Libraries-Geo10x6-B3-MultipleA_S14_L001_R1_001.fastq.gz --in2 10x-Genomics-Libraries-Geo10x6-B3-MultipleA_S14_L001_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html 10x-Genomics-Libraries-Geo10x6-B3-MultipleA_S14_L001}.fastp-trim.20210401.report.html --json 10x-Genomics-Libraries-Geo10x6-B3-MultipleA_S14_L001.fastp-trim.20210401.report.json --out1 10x-Genomics-Libraries-Geo10x6-B3-MultipleA_S14_L001_R1_001.fastp-trim.20210401.fq.gz --out2 10x-Genomics-Libraries-Geo10x6-B3-MultipleA_S14_L001_R2_001.fastp-trim.20210401.fq.gz 
10x-Genomics-Libraries-Geo10x6-B3-MultipleA_S14_L002	/gscratch/srlab/programs/fastp-0.20.0/fastp --in1 10x-Genomics-Libraries-Geo10x6-B3-MultipleA_S14_L002_R1_001.fastq.gz --in2 10x-Genomics-Libraries-Geo10x6-B3-MultipleA_S14_L002_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html 10x-Genomics-Libraries-Geo10x6-B3-MultipleA_S14_L002}.fastp-trim.20210401.report.html --json 10x-Genomics-Libraries-Geo10x6-B3-MultipleA_S14_L002.fastp-trim.20210401.report.json --out1 10x-Genomics-Libraries-Geo10x6-B3-MultipleA_S14_L002_R1_001.fastp-trim.20210401.fq.gz --out2 10x-Genomics-Libraries-Geo10x6-B3-MultipleA_S14_L002_R2_001.fastp-trim.20210401.fq.gz 
10x-Genomics-Libraries-Geo10x6-B3-MultipleB_S15_L001	/gscratch/srlab/programs/fastp-0.20.0/fastp --in1 10x-Genomics-Libraries-Geo10x6-B3-MultipleB_S15_L001_R1_001.fastq.gz --in2 10x-Genomics-Libraries-Geo10x6-B3-MultipleB_S15_L001_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html 10x-Genomics-Libraries-Geo10x6-B3-MultipleB_S15_L001}.fastp-trim.20210401.report.html --json 10x-Genomics-Libraries-Geo10x6-B3-MultipleB_S15_L001.fastp-trim.20210401.report.json --out1 10x-Genomics-Libraries-Geo10x6-B3-MultipleB_S15_L001_R1_001.fastp-trim.20210401.fq.gz --out2 10x-Genomics-Libraries-Geo10x6-B3-MultipleB_S15_L001_R2_001.fastp-trim.20210401.fq.gz 
10x-Genomics-Libraries-Geo10x6-B3-MultipleB_S15_L002	/gscratch/srlab/programs/fastp-0.20.0/fastp --in1 10x-Genomics-Libraries-Geo10x6-B3-MultipleB_S15_L002_R1_001.fastq.gz --in2 10x-Genomics-Libraries-Geo10x6-B3-MultipleB_S15_L002_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html 10x-Genomics-Libraries-Geo10x6-B3-MultipleB_S15_L002}.fastp-trim.20210401.report.html --json 10x-Genomics-Libraries-Geo10x6-B3-MultipleB_S15_L002.fastp-trim.20210401.report.json --out1 10x-Genomics-Libraries-Geo10x6-B3-MultipleB_S15_L002_R1_001.fastp-trim.20210401.fq.gz --out2 10x-Genomics-Libraries-Geo10x6-B3-MultipleB_S15_L002_R2_001.fastp-trim.20210401.fq.gz 
10x-Genomics-Libraries-Geo10x6-B3-MultipleC_S16_L001	/gscratch/srlab/programs/fastp-0.20.0/fastp --in1 10x-Genomics-Libraries-Geo10x6-B3-MultipleC_S16_L001_R1_001.fastq.gz --in2 10x-Genomics-Libraries-Geo10x6-B3-MultipleC_S16_L001_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html 10x-Genomics-Libraries-Geo10x6-B3-MultipleC_S16_L001}.fastp-trim.20210401.report.html --json 10x-Genomics-Libraries-Geo10x6-B3-MultipleC_S16_L001.fastp-trim.20210401.report.json --out1 10x-Genomics-Libraries-Geo10x6-B3-MultipleC_S16_L001_R1_001.fastp-trim.20210401.fq.gz --out2 10x-Genomics-Libraries-Geo10x6-B3-MultipleC_S16_L001_R2_001.fastp-trim.20210401.fq.gz 
10x-Genomics-Libraries-Geo10x6-B3-MultipleC_S16_L002	/gscratch/srlab/programs/fastp-0.20.0/fastp --in1 10x-Genomics-Libraries-Geo10x6-B3-MultipleC_S16_L002_R1_001.fastq.gz --in2 10x-Genomics-Libraries-Geo10x6-B3-MultipleC_S16_L002_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html 10x-Genomics-Libraries-Geo10x6-B3-MultipleC_S16_L002}.fastp-trim.20210401.report.html --json 10x-Genomics-Libraries-Geo10x6-B3-MultipleC_S16_L002.fastp-trim.20210401.report.json --out1 10x-Genomics-Libraries-Geo10x6-B3-MultipleC_S16_L002_R1_001.fastp-trim.20210401.fq.gz --out2 10x-Genomics-Libraries-Geo10x6-B3-MultipleC_S16_L002_R2_001.fastp-trim.20210401.fq.gz 
10x-Genomics-Libraries-Geo10x6-B3-MultipleD_S17_L001	/gscratch/srlab/programs/fastp-0.20.0/fastp --in1 10x-Genomics-Libraries-Geo10x6-B3-MultipleD_S17_L001_R1_001.fastq.gz --in2 10x-Genomics-Libraries-Geo10x6-B3-MultipleD_S17_L001_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html 10x-Genomics-Libraries-Geo10x6-B3-MultipleD_S17_L001}.fastp-trim.20210401.report.html --json 10x-Genomics-Libraries-Geo10x6-B3-MultipleD_S17_L001.fastp-trim.20210401.report.json --out1 10x-Genomics-Libraries-Geo10x6-B3-MultipleD_S17_L001_R1_001.fastp-trim.20210401.fq.gz --out2 10x-Genomics-Libraries-Geo10x6-B3-MultipleD_S17_L001_R2_001.fastp-trim.20210401.fq.gz 
10x-Genomics-Libraries-Geo10x6-B3-MultipleD_S17_L002	/gscratch/srlab/programs/fastp-0.20.0/fastp --in1 10x-Genomics-Libraries-Geo10x6-B3-MultipleD_S17_L002_R1_001.fastq.gz --in2 10x-Genomics-Libraries-Geo10x6-B3-MultipleD_S17_L002_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html 10x-Genomics-Libraries-Geo10x6-B3-MultipleD_S17_L002}.fastp-trim.20210401.report.html --json 10x-Genomics-Libraries-Geo10x6-B3-MultipleD_S17_L002.fastp-trim.20210401.report.json --out1 10x-Genomics-Libraries-Geo10x6-B3-MultipleD_S17_L002_R1_001.fastp-trim.20210401.fq.gz --out2 10x-Genomics-Libraries-Geo10x6-B3-MultipleD_S17_L002_R2_001.fastp-trim.20210401.fq.gz 
Geoduck_HiC_S2_L002	/gscratch/srlab/programs/fastp-0.20.0/fastp --in1 Geoduck_HiC_S2_L002_R1_001.fastq.gz --in2 Geoduck_HiC_S2_L002_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html Geoduck_HiC_S2_L002}.fastp-trim.20210401.report.html --json Geoduck_HiC_S2_L002.fastp-trim.20210401.report.json --out1 Geoduck_HiC_S2_L002_R1_001.fastp-trim.20210401.fq.gz --out2 Geoduck_HiC_S2_L002_R2_001.fastp-trim.20210401.fq.gz 
Geoduck_HiC_S2_L006	/gscratch/srlab/programs/fastp-0.20.0/fastp --in1 Geoduck_HiC_S2_L006_R1_001.fastq.gz --in2 Geoduck_HiC_S2_L006_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html Geoduck_HiC_S2_L006}.fastp-trim.20210401.report.html --json Geoduck_HiC_S2_L006.fastp-trim.20210401.report.json --out1 Geoduck_HiC_S2_L006_R1_001.fastp-trim.20210401.fq.gz --out2 Geoduck_HiC_S2_L006_R2_001.fastp-trim.20210401.fq.gz 
HiC-Libraries-GeoHiC-C3-N701_S18_L001	/gscratch/srlab/programs/fastp-0.20.0/fastp --in1 HiC-Libraries-GeoHiC-C3-N701_S18_L001_R1_001.fastq.gz --in2 HiC-Libraries-GeoHiC-C3-N701_S18_L001_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html HiC-Libraries-GeoHiC-C3-N701_S18_L001}.fastp-trim.20210401.report.html --json HiC-Libraries-GeoHiC-C3-N701_S18_L001.fastp-trim.20210401.report.json --out1 HiC-Libraries-GeoHiC-C3-N701_S18_L001_R1_001.fastp-trim.20210401.fq.gz --out2 HiC-Libraries-GeoHiC-C3-N701_S18_L001_R2_001.fastp-trim.20210401.fq.gz 
HiC-Libraries-GeoHiC-C3-N701_S18_L002	/gscratch/srlab/programs/fastp-0.20.0/fastp --in1 HiC-Libraries-GeoHiC-C3-N701_S18_L002_R1_001.fastq.gz --in2 HiC-Libraries-GeoHiC-C3-N701_S18_L002_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html HiC-Libraries-GeoHiC-C3-N701_S18_L002}.fastp-trim.20210401.report.html --json HiC-Libraries-GeoHiC-C3-N701_S18_L002.fastp-trim.20210401.report.json --out1 HiC-Libraries-GeoHiC-C3-N701_S18_L002_R1_001.fastp-trim.20210401.fq.gz --out2 HiC-Libraries-GeoHiC-C3-N701_S18_L002_R2_001.fastp-trim.20210401.fq.gz