Sample	command
45937_Exp215_GHEtest_1_S1_IPSC_mRNA_A21	fastp -w 2 --in1 /scratch/slrinzema/ghe_2024/samples/45937_Exp215_GHEtest_1_S1_IPSC_mRNA_A21_R1.fastq.gz --in2 /scratch/slrinzema/ghe_2024/samples/45937_Exp215_GHEtest_1_S1_IPSC_mRNA_A21_R2.fastq.gz --out1 /scratch/slrinzema/ghe_2024/results/fastq_trimmed/45937_Exp215_GHEtest_1_S1_IPSC_mRNA_A21_R1_trimmed.fastq.gz --out2 /scratch/slrinzema/ghe_2024/results/fastq_trimmed/45937_Exp215_GHEtest_1_S1_IPSC_mRNA_A21_R2_trimmed.fastq.gz -h /scratch/slrinzema/ghe_2024/results/qc/trimming/45937_Exp215_GHEtest_1_S1_IPSC_mRNA_A21.fastp.html -j /scratch/slrinzema/ghe_2024/results/qc/trimming/45937_Exp215_GHEtest_1_S1_IPSC_mRNA_A21.fastp.json 
45938_Exp215_GHEtest_2_S2_IPSC_mRNA_A22	fastp -w 2 --in1 /scratch/slrinzema/ghe_2024/samples/45938_Exp215_GHEtest_2_S2_IPSC_mRNA_A22_R1.fastq.gz --in2 /scratch/slrinzema/ghe_2024/samples/45938_Exp215_GHEtest_2_S2_IPSC_mRNA_A22_R2.fastq.gz --out1 /scratch/slrinzema/ghe_2024/results/fastq_trimmed/45938_Exp215_GHEtest_2_S2_IPSC_mRNA_A22_R1_trimmed.fastq.gz --out2 /scratch/slrinzema/ghe_2024/results/fastq_trimmed/45938_Exp215_GHEtest_2_S2_IPSC_mRNA_A22_R2_trimmed.fastq.gz -h /scratch/slrinzema/ghe_2024/results/qc/trimming/45938_Exp215_GHEtest_2_S2_IPSC_mRNA_A22.fastp.html -j /scratch/slrinzema/ghe_2024/results/qc/trimming/45938_Exp215_GHEtest_2_S2_IPSC_mRNA_A22.fastp.json 
45939_Exp215_GHEtest_3_S1_IPSC_noRibo_A23	fastp -w 2 --in1 /scratch/slrinzema/ghe_2024/samples/45939_Exp215_GHEtest_3_S1_IPSC_noRibo_A23_R1.fastq.gz --in2 /scratch/slrinzema/ghe_2024/samples/45939_Exp215_GHEtest_3_S1_IPSC_noRibo_A23_R2.fastq.gz --out1 /scratch/slrinzema/ghe_2024/results/fastq_trimmed/45939_Exp215_GHEtest_3_S1_IPSC_noRibo_A23_R1_trimmed.fastq.gz --out2 /scratch/slrinzema/ghe_2024/results/fastq_trimmed/45939_Exp215_GHEtest_3_S1_IPSC_noRibo_A23_R2_trimmed.fastq.gz -h /scratch/slrinzema/ghe_2024/results/qc/trimming/45939_Exp215_GHEtest_3_S1_IPSC_noRibo_A23.fastp.html -j /scratch/slrinzema/ghe_2024/results/qc/trimming/45939_Exp215_GHEtest_3_S1_IPSC_noRibo_A23.fastp.json 
45940_Exp215_GHEtest_4_S2_IPSC_noRibo_A24	fastp -w 2 --in1 /scratch/slrinzema/ghe_2024/samples/45940_Exp215_GHEtest_4_S2_IPSC_noRibo_A24_R1.fastq.gz --in2 /scratch/slrinzema/ghe_2024/samples/45940_Exp215_GHEtest_4_S2_IPSC_noRibo_A24_R2.fastq.gz --out1 /scratch/slrinzema/ghe_2024/results/fastq_trimmed/45940_Exp215_GHEtest_4_S2_IPSC_noRibo_A24_R1_trimmed.fastq.gz --out2 /scratch/slrinzema/ghe_2024/results/fastq_trimmed/45940_Exp215_GHEtest_4_S2_IPSC_noRibo_A24_R2_trimmed.fastq.gz -h /scratch/slrinzema/ghe_2024/results/qc/trimming/45940_Exp215_GHEtest_4_S2_IPSC_noRibo_A24.fastp.html -j /scratch/slrinzema/ghe_2024/results/qc/trimming/45940_Exp215_GHEtest_4_S2_IPSC_noRibo_A24.fastp.json 
45941_Exp215_GHEtest_5_S2_IPSC_noRibo_A01	fastp -w 2 --in1 /scratch/slrinzema/ghe_2024/samples/45941_Exp215_GHEtest_5_S2_IPSC_noRibo_A01_R1.fastq.gz --in2 /scratch/slrinzema/ghe_2024/samples/45941_Exp215_GHEtest_5_S2_IPSC_noRibo_A01_R2.fastq.gz --out1 /scratch/slrinzema/ghe_2024/results/fastq_trimmed/45941_Exp215_GHEtest_5_S2_IPSC_noRibo_A01_R1_trimmed.fastq.gz --out2 /scratch/slrinzema/ghe_2024/results/fastq_trimmed/45941_Exp215_GHEtest_5_S2_IPSC_noRibo_A01_R2_trimmed.fastq.gz -h /scratch/slrinzema/ghe_2024/results/qc/trimming/45941_Exp215_GHEtest_5_S2_IPSC_noRibo_A01.fastp.html -j /scratch/slrinzema/ghe_2024/results/qc/trimming/45941_Exp215_GHEtest_5_S2_IPSC_noRibo_A01.fastp.json 
45942_Exp215_GHEtest_6_S2_IPSC_noRibo_A02	fastp -w 2 --in1 /scratch/slrinzema/ghe_2024/samples/45942_Exp215_GHEtest_6_S2_IPSC_noRibo_A02_R1.fastq.gz --in2 /scratch/slrinzema/ghe_2024/samples/45942_Exp215_GHEtest_6_S2_IPSC_noRibo_A02_R2.fastq.gz --out1 /scratch/slrinzema/ghe_2024/results/fastq_trimmed/45942_Exp215_GHEtest_6_S2_IPSC_noRibo_A02_R1_trimmed.fastq.gz --out2 /scratch/slrinzema/ghe_2024/results/fastq_trimmed/45942_Exp215_GHEtest_6_S2_IPSC_noRibo_A02_R2_trimmed.fastq.gz -h /scratch/slrinzema/ghe_2024/results/qc/trimming/45942_Exp215_GHEtest_6_S2_IPSC_noRibo_A02.fastp.html -j /scratch/slrinzema/ghe_2024/results/qc/trimming/45942_Exp215_GHEtest_6_S2_IPSC_noRibo_A02.fastp.json