Sample	command
45943_Exp215_GHEtest_7_S1_Arabidopsis__RiboErase_220_A04	fastp -w 2 --in1 /scratch/slrinzema/ghe_2024/samples/45943_Exp215_GHEtest_7_S1_Arabidopsis__RiboErase_220_A04_R1.fastq.gz --in2 /scratch/slrinzema/ghe_2024/samples/45943_Exp215_GHEtest_7_S1_Arabidopsis__RiboErase_220_A04_R2.fastq.gz --out1 /scratch/slrinzema/ghe_2024/results/fastq_trimmed/45943_Exp215_GHEtest_7_S1_Arabidopsis__RiboErase_220_A04_R1_trimmed.fastq.gz --out2 /scratch/slrinzema/ghe_2024/results/fastq_trimmed/45943_Exp215_GHEtest_7_S1_Arabidopsis__RiboErase_220_A04_R2_trimmed.fastq.gz -h /scratch/slrinzema/ghe_2024/results/qc/trimming/45943_Exp215_GHEtest_7_S1_Arabidopsis__RiboErase_220_A04.fastp.html -j /scratch/slrinzema/ghe_2024/results/qc/trimming/45943_Exp215_GHEtest_7_S1_Arabidopsis__RiboErase_220_A04.fastp.json 
45944_Exp215_GHEtest_8_S2_Arabidopsis_RiboErase_290_A09	fastp -w 2 --in1 /scratch/slrinzema/ghe_2024/samples/45944_Exp215_GHEtest_8_S2_Arabidopsis_RiboErase_290_A09_R1.fastq.gz --in2 /scratch/slrinzema/ghe_2024/samples/45944_Exp215_GHEtest_8_S2_Arabidopsis_RiboErase_290_A09_R2.fastq.gz --out1 /scratch/slrinzema/ghe_2024/results/fastq_trimmed/45944_Exp215_GHEtest_8_S2_Arabidopsis_RiboErase_290_A09_R1_trimmed.fastq.gz --out2 /scratch/slrinzema/ghe_2024/results/fastq_trimmed/45944_Exp215_GHEtest_8_S2_Arabidopsis_RiboErase_290_A09_R2_trimmed.fastq.gz -h /scratch/slrinzema/ghe_2024/results/qc/trimming/45944_Exp215_GHEtest_8_S2_Arabidopsis_RiboErase_290_A09.fastp.html -j /scratch/slrinzema/ghe_2024/results/qc/trimming/45944_Exp215_GHEtest_8_S2_Arabidopsis_RiboErase_290_A09.fastp.json 
45945_Exp215_GHEtest_11_S1_Arabidopsis_noRibo_A27	fastp -w 2 --in1 /scratch/slrinzema/ghe_2024/samples/45945_Exp215_GHEtest_11_S1_Arabidopsis_noRibo_A27_R1.fastq.gz --in2 /scratch/slrinzema/ghe_2024/samples/45945_Exp215_GHEtest_11_S1_Arabidopsis_noRibo_A27_R2.fastq.gz --out1 /scratch/slrinzema/ghe_2024/results/fastq_trimmed/45945_Exp215_GHEtest_11_S1_Arabidopsis_noRibo_A27_R1_trimmed.fastq.gz --out2 /scratch/slrinzema/ghe_2024/results/fastq_trimmed/45945_Exp215_GHEtest_11_S1_Arabidopsis_noRibo_A27_R2_trimmed.fastq.gz -h /scratch/slrinzema/ghe_2024/results/qc/trimming/45945_Exp215_GHEtest_11_S1_Arabidopsis_noRibo_A27.fastp.html -j /scratch/slrinzema/ghe_2024/results/qc/trimming/45945_Exp215_GHEtest_11_S1_Arabidopsis_noRibo_A27.fastp.json 
45946_Exp215_GHEtest_12_S2_Arabidopsis_noRibo_A31	fastp -w 2 --in1 /scratch/slrinzema/ghe_2024/samples/45946_Exp215_GHEtest_12_S2_Arabidopsis_noRibo_A31_R1.fastq.gz --in2 /scratch/slrinzema/ghe_2024/samples/45946_Exp215_GHEtest_12_S2_Arabidopsis_noRibo_A31_R2.fastq.gz --out1 /scratch/slrinzema/ghe_2024/results/fastq_trimmed/45946_Exp215_GHEtest_12_S2_Arabidopsis_noRibo_A31_R1_trimmed.fastq.gz --out2 /scratch/slrinzema/ghe_2024/results/fastq_trimmed/45946_Exp215_GHEtest_12_S2_Arabidopsis_noRibo_A31_R2_trimmed.fastq.gz -h /scratch/slrinzema/ghe_2024/results/qc/trimming/45946_Exp215_GHEtest_12_S2_Arabidopsis_noRibo_A31.fastp.html -j /scratch/slrinzema/ghe_2024/results/qc/trimming/45946_Exp215_GHEtest_12_S2_Arabidopsis_noRibo_A31.fastp.json