Sample	command
Xt_stage105_rep2	fastp -w 2 --in1 /bank/raw/xenopus/Xt_stage105_rep2_R1.fastq.gz --in2 /bank/raw/xenopus/Xt_stage105_rep2_R2.fastq.gz --out1 /bank/experiments/2021-10/xt_atac/results/fastq_trimmed/Xt_stage105_rep2_R1_trimmed.fastq.gz --out2 /bank/experiments/2021-10/xt_atac/results/fastq_trimmed/Xt_stage105_rep2_R2_trimmed.fastq.gz -h /bank/experiments/2021-10/xt_atac/results/qc/trimming/Xt_stage105_rep2.fastp.html -j /bank/experiments/2021-10/xt_atac/results/qc/trimming/Xt_stage105_rep2.fastp.json 
Xt_stage105_rep3	fastp -w 2 --in1 /bank/raw/xenopus/Xt_stage105_rep3_R1.fastq.gz --in2 /bank/raw/xenopus/Xt_stage105_rep3_R2.fastq.gz --out1 /bank/experiments/2021-10/xt_atac/results/fastq_trimmed/Xt_stage105_rep3_R1_trimmed.fastq.gz --out2 /bank/experiments/2021-10/xt_atac/results/fastq_trimmed/Xt_stage105_rep3_R2_trimmed.fastq.gz -h /bank/experiments/2021-10/xt_atac/results/qc/trimming/Xt_stage105_rep3.fastp.html -j /bank/experiments/2021-10/xt_atac/results/qc/trimming/Xt_stage105_rep3.fastp.json 
Xt_stage12_rep1	fastp -w 2 --in1 /bank/raw/xenopus/Xt_stage12_rep1_R1.fastq.gz --in2 /bank/raw/xenopus/Xt_stage12_rep1_R2.fastq.gz --out1 /bank/experiments/2021-10/xt_atac/results/fastq_trimmed/Xt_stage12_rep1_R1_trimmed.fastq.gz --out2 /bank/experiments/2021-10/xt_atac/results/fastq_trimmed/Xt_stage12_rep1_R2_trimmed.fastq.gz -h /bank/experiments/2021-10/xt_atac/results/qc/trimming/Xt_stage12_rep1.fastp.html -j /bank/experiments/2021-10/xt_atac/results/qc/trimming/Xt_stage12_rep1.fastp.json 
Xt_stage12_rep2	fastp -w 2 --in1 /bank/raw/xenopus/Xt_stage12_rep2_R1.fastq.gz --in2 /bank/raw/xenopus/Xt_stage12_rep2_R2.fastq.gz --out1 /bank/experiments/2021-10/xt_atac/results/fastq_trimmed/Xt_stage12_rep2_R1_trimmed.fastq.gz --out2 /bank/experiments/2021-10/xt_atac/results/fastq_trimmed/Xt_stage12_rep2_R2_trimmed.fastq.gz -h /bank/experiments/2021-10/xt_atac/results/qc/trimming/Xt_stage12_rep2.fastp.html -j /bank/experiments/2021-10/xt_atac/results/qc/trimming/Xt_stage12_rep2.fastp.json 
Xt_stage16_rep1	fastp -w 2 --in1 /bank/raw/xenopus/Xt_stage16_rep1_R1.fastq.gz --in2 /bank/raw/xenopus/Xt_stage16_rep1_R2.fastq.gz --out1 /bank/experiments/2021-10/xt_atac/results/fastq_trimmed/Xt_stage16_rep1_R1_trimmed.fastq.gz --out2 /bank/experiments/2021-10/xt_atac/results/fastq_trimmed/Xt_stage16_rep1_R2_trimmed.fastq.gz -h /bank/experiments/2021-10/xt_atac/results/qc/trimming/Xt_stage16_rep1.fastp.html -j /bank/experiments/2021-10/xt_atac/results/qc/trimming/Xt_stage16_rep1.fastp.json 
Xt_stage16_rep2	fastp -w 2 --in1 /bank/raw/xenopus/Xt_stage16_rep2_R1.fastq.gz --in2 /bank/raw/xenopus/Xt_stage16_rep2_R2.fastq.gz --out1 /bank/experiments/2021-10/xt_atac/results/fastq_trimmed/Xt_stage16_rep2_R1_trimmed.fastq.gz --out2 /bank/experiments/2021-10/xt_atac/results/fastq_trimmed/Xt_stage16_rep2_R2_trimmed.fastq.gz -h /bank/experiments/2021-10/xt_atac/results/qc/trimming/Xt_stage16_rep2.fastp.html -j /bank/experiments/2021-10/xt_atac/results/qc/trimming/Xt_stage16_rep2.fastp.json 
Xt_stage26_rep1	fastp -w 2 --in1 /bank/raw/xenopus/Xt_stage26_rep1_R1.fastq.gz --in2 /bank/raw/xenopus/Xt_stage26_rep1_R2.fastq.gz --out1 /bank/experiments/2021-10/xt_atac/results/fastq_trimmed/Xt_stage26_rep1_R1_trimmed.fastq.gz --out2 /bank/experiments/2021-10/xt_atac/results/fastq_trimmed/Xt_stage26_rep1_R2_trimmed.fastq.gz -h /bank/experiments/2021-10/xt_atac/results/qc/trimming/Xt_stage26_rep1.fastp.html -j /bank/experiments/2021-10/xt_atac/results/qc/trimming/Xt_stage26_rep1.fastp.json 
Xt_stage26_rep2	fastp -w 2 --in1 /bank/raw/xenopus/Xt_stage26_rep2_R1.fastq.gz --in2 /bank/raw/xenopus/Xt_stage26_rep2_R2.fastq.gz --out1 /bank/experiments/2021-10/xt_atac/results/fastq_trimmed/Xt_stage26_rep2_R1_trimmed.fastq.gz --out2 /bank/experiments/2021-10/xt_atac/results/fastq_trimmed/Xt_stage26_rep2_R2_trimmed.fastq.gz -h /bank/experiments/2021-10/xt_atac/results/qc/trimming/Xt_stage26_rep2.fastp.html -j /bank/experiments/2021-10/xt_atac/results/qc/trimming/Xt_stage26_rep2.fastp.json 
Xt_stage34_rep1	fastp -w 2 --in1 /bank/raw/xenopus/Xt_stage34_rep1_R1.fastq.gz --in2 /bank/raw/xenopus/Xt_stage34_rep1_R2.fastq.gz --out1 /bank/experiments/2021-10/xt_atac/results/fastq_trimmed/Xt_stage34_rep1_R1_trimmed.fastq.gz --out2 /bank/experiments/2021-10/xt_atac/results/fastq_trimmed/Xt_stage34_rep1_R2_trimmed.fastq.gz -h /bank/experiments/2021-10/xt_atac/results/qc/trimming/Xt_stage34_rep1.fastp.html -j /bank/experiments/2021-10/xt_atac/results/qc/trimming/Xt_stage34_rep1.fastp.json 
Xt_stage34_rep2	fastp -w 2 --in1 /bank/raw/xenopus/Xt_stage34_rep2_R1.fastq.gz --in2 /bank/raw/xenopus/Xt_stage34_rep2_R2.fastq.gz --out1 /bank/experiments/2021-10/xt_atac/results/fastq_trimmed/Xt_stage34_rep2_R1_trimmed.fastq.gz --out2 /bank/experiments/2021-10/xt_atac/results/fastq_trimmed/Xt_stage34_rep2_R2_trimmed.fastq.gz -h /bank/experiments/2021-10/xt_atac/results/qc/trimming/Xt_stage34_rep2.fastp.html -j /bank/experiments/2021-10/xt_atac/results/qc/trimming/Xt_stage34_rep2.fastp.json 
Xt_stage9_rep2	fastp -w 2 --in1 /bank/raw/xenopus/Xt_stage9_rep2_R1.fastq.gz --in2 /bank/raw/xenopus/Xt_stage9_rep2_R2.fastq.gz --out1 /bank/experiments/2021-10/xt_atac/results/fastq_trimmed/Xt_stage9_rep2_R1_trimmed.fastq.gz --out2 /bank/experiments/2021-10/xt_atac/results/fastq_trimmed/Xt_stage9_rep2_R2_trimmed.fastq.gz -h /bank/experiments/2021-10/xt_atac/results/qc/trimming/Xt_stage9_rep2.fastp.html -j /bank/experiments/2021-10/xt_atac/results/qc/trimming/Xt_stage9_rep2.fastp.json