#template
#example from:https://github.com/marcelm/cutadapt/issues/96
#cutadapt -c -a CGCCTTGGCCGTACAGCAG
#/data/results/tools/adapter/cutadapt-1.9.1/bin/cutadapt -q 20 -z -m 15 -c -a CGCCTTGGCCGTACAGCAG ../Backup_Polysomes_TTP/ /data/images/proton/DKlab/polysomes/reads/Backup_Polysomes_TTP/ >& .log > .fastq
#manual /data/results/tools/adapter/cutadapt-1.9.1/bin/cutadapt -q 20 -z -m 15 -c -a CGCCTTGGCCGTACAGCAG ../Backup_Polysomes_TTP/ugc_623_BC_FRAG_W_Paulina_150506_L02_ugc_623_9_F3.csfasta /data/images/proton/DKlab/polysomes/reads/Backup_Polysomes_TTP/ugc_623_BC_FRAG_W_Paulina_150506_L02_ugc_623_9_F3.QV.qual >& 0hrep1b.log > 0hrep1b.fastq
/data/results/tools/adapter/cutadapt-1.9.1/bin/cutadapt -q 20 -z -m 15 -c -a CGCCTTGGCCGTACAGCAG ../Backup_Polysomes_TTP/ugc_623_BC_FRAG_W_Paulina_150506_L02_ugc_623_10_F3.csfasta /data/images/proton/DKlab/polysomes/reads/Backup_Polysomes_TTP/ugc_623_BC_FRAG_W_Paulina_150506_L02_ugc_623_10_F3.QV.qual >& WT_0h_replicate_II.log > WT_0h_replicate_II.fastq
/data/results/tools/adapter/cutadapt-1.9.1/bin/cutadapt -q 20 -z -m 15 -c -a CGCCTTGGCCGTACAGCAG ../Backup_Polysomes_TTP/ugc_623_BC_FRAG_W_Paulina_150506_L02_ugc_623_11_F3.csfasta /data/images/proton/DKlab/polysomes/reads/Backup_Polysomes_TTP/ugc_623_BC_FRAG_W_Paulina_150506_L02_ugc_623_11_F3.QV.qual >& WT_2h_replicate_I.log > WT_2h_replicate_I.fastq
/data/results/tools/adapter/cutadapt-1.9.1/bin/cutadapt -q 20 -z -m 15 -c -a CGCCTTGGCCGTACAGCAG ../Backup_Polysomes_TTP/ugc_623_BC_FRAG_W_Paulina_150506_L02_ugc_623_12_F3.csfasta /data/images/proton/DKlab/polysomes/reads/Backup_Polysomes_TTP/ugc_623_BC_FRAG_W_Paulina_150506_L02_ugc_623_12_F3.QV.qual >& WT_2h_replicate_II.log > WT_2h_replicate_II.fastq
/data/results/tools/adapter/cutadapt-1.9.1/bin/cutadapt -q 20 -z -m 15 -c -a CGCCTTGGCCGTACAGCAG ../Backup_Polysomes_TTP/ugc_623_BC_FRAG_W_Paulina_150506_L02_ugc_623_13_F3.csfasta /data/images/proton/DKlab/polysomes/reads/Backup_Polysomes_TTP/ugc_623_BC_FRAG_W_Paulina_150506_L02_ugc_623_13_F3.QV.qual >& WT_6h_replicate_I.log > WT_6h_replicate_I.fastq
/data/results/tools/adapter/cutadapt-1.9.1/bin/cutadapt -q 20 -z -m 15 -c -a CGCCTTGGCCGTACAGCAG ../Backup_Polysomes_TTP/ugc_623_BC_FRAG_W_Paulina_150506_L02_ugc_623_14_F3.csfasta /data/images/proton/DKlab/polysomes/reads/Backup_Polysomes_TTP/ugc_623_BC_FRAG_W_Paulina_150506_L02_ugc_623_14_F3.QV.qual >& WT_6h_replicate_II.log > WT_6h_replicate_II.fastq
/data/results/tools/adapter/cutadapt-1.9.1/bin/cutadapt -q 20 -z -m 15 -c -a CGCCTTGGCCGTACAGCAG ../Backup_Polysomes_TTP/ugc_623_BC_FRAG_W_Paulina_150506_L02_ugc_623_15_F3.csfasta /data/images/proton/DKlab/polysomes/reads/Backup_Polysomes_TTP/ugc_623_BC_FRAG_W_Paulina_150506_L02_ugc_623_15_F3.QV.qual >& WT_IL4_replicate_I.log > WT_IL4_replicate_I.fastq
/data/results/tools/adapter/cutadapt-1.9.1/bin/cutadapt -q 20 -z -m 15 -c -a CGCCTTGGCCGTACAGCAG ../Backup_Polysomes_TTP/ugc_623_BC_FRAG_W_Paulina_150506_L02_ugc_623_16_F3.csfasta /data/images/proton/DKlab/polysomes/reads/Backup_Polysomes_TTP/ugc_623_BC_FRAG_W_Paulina_150506_L02_ugc_623_16_F3.QV.qual >& WT_IL4_replicate_II.log > WT_IL4_replicate_II.fastq
/data/results/tools/adapter/cutadapt-1.9.1/bin/cutadapt -q 20 -z -m 15 -c -a CGCCTTGGCCGTACAGCAG ../Backup_Polysomes_TTP/ugc_623_BC_FRAG_W_Paulina_150506_L02_ugc_623_17_F3.csfasta /data/images/proton/DKlab/polysomes/reads/Backup_Polysomes_TTP/ugc_623_BC_FRAG_W_Paulina_150506_L02_ugc_623_17_F3.QV.qual >& WT_IFN-gamma_replicate_I.log > WT_IFN-gamma_replicate_I.fastq
/data/results/tools/adapter/cutadapt-1.9.1/bin/cutadapt -q 20 -z -m 15 -c -a CGCCTTGGCCGTACAGCAG ../Backup_Polysomes_TTP/ugc_623_BC_FRAG_W_Paulina_150506_L02_ugc_623_18_F3.csfasta /data/images/proton/DKlab/polysomes/reads/Backup_Polysomes_TTP/ugc_623_BC_FRAG_W_Paulina_150506_L02_ugc_623_18_F3.QV.qual >& WT_IFN-gamma_replicate_II.log > WT_IFN-gamma_replicate_II.fastq
/data/results/tools/adapter/cutadapt-1.9.1/bin/cutadapt -q 20 -z -m 15 -c -a CGCCTTGGCCGTACAGCAG ../Backup_Polysomes_TTP/ugc_623_BC_FRAG_W_Paulina_150506_L02_ugc_623_9_F3.csfasta /data/images/proton/DKlab/polysomes/reads/Backup_Polysomes_TTP/ugc_623_BC_FRAG_W_Paulina_150506_L02_ugc_623_9_F3.QV.qual >& WT_0h_replicate_I.log > WT_0h_replicate_I.fastq
/data/results/tools/adapter/cutadapt-1.9.1/bin/cutadapt -q 20 -z -m 15 -c -a CGCCTTGGCCGTACAGCAG ../Backup_Polysomes_TTP/ugc_623_BC_FRAG_W_Paulina_150506_L03_ugc_623_19_F3.csfasta /data/images/proton/DKlab/polysomes/reads/Backup_Polysomes_TTP/ugc_623_BC_FRAG_W_Paulina_150506_L03_ugc_623_19_F3.QV.qual >& ΚΟ_0h_replicate_I.log > ΚΟ_0h_replicate_I.fastq
/data/results/tools/adapter/cutadapt-1.9.1/bin/cutadapt -q 20 -z -m 15 -c -a CGCCTTGGCCGTACAGCAG ../Backup_Polysomes_TTP/ugc_623_BC_FRAG_W_Paulina_150506_L03_ugc_623_20_F3.csfasta /data/images/proton/DKlab/polysomes/reads/Backup_Polysomes_TTP/ugc_623_BC_FRAG_W_Paulina_150506_L03_ugc_623_20_F3.QV.qual >& KO_0h_replicate_II.log > KO_0h_replicate_II.fastq
/data/results/tools/adapter/cutadapt-1.9.1/bin/cutadapt -q 20 -z -m 15 -c -a CGCCTTGGCCGTACAGCAG ../Backup_Polysomes_TTP/ugc_623_BC_FRAG_W_Paulina_150506_L03_ugc_623_21_F3.csfasta /data/images/proton/DKlab/polysomes/reads/Backup_Polysomes_TTP/ugc_623_BC_FRAG_W_Paulina_150506_L03_ugc_623_21_F3.QV.qual >& KO_2h_replicate_I.log > KO_2h_replicate_I.fastq
/data/results/tools/adapter/cutadapt-1.9.1/bin/cutadapt -q 20 -z -m 15 -c -a CGCCTTGGCCGTACAGCAG ../Backup_Polysomes_TTP/ugc_623_BC_FRAG_W_Paulina_150506_L03_ugc_623_22_F3.csfasta /data/images/proton/DKlab/polysomes/reads/Backup_Polysomes_TTP/ugc_623_BC_FRAG_W_Paulina_150506_L03_ugc_623_22_F3.QV.qual >& KO_2h_replicate_II.log > KO_2h_replicate_II.fastq
/data/results/tools/adapter/cutadapt-1.9.1/bin/cutadapt -q 20 -z -m 15 -c -a CGCCTTGGCCGTACAGCAG ../Backup_Polysomes_TTP/ugc_623_BC_FRAG_W_Paulina_150506_L03_ugc_623_23_F3.csfasta /data/images/proton/DKlab/polysomes/reads/Backup_Polysomes_TTP/ugc_623_BC_FRAG_W_Paulina_150506_L03_ugc_623_23_F3.QV.qual >& KO_6h_replicate_I.log > KO_6h_replicate_I.fastq
/data/results/tools/adapter/cutadapt-1.9.1/bin/cutadapt -q 20 -z -m 15 -c -a CGCCTTGGCCGTACAGCAG ../Backup_Polysomes_TTP/ugc_623_BC_FRAG_W_Paulina_150506_L03_ugc_623_24_F3.csfasta /data/images/proton/DKlab/polysomes/reads/Backup_Polysomes_TTP/ugc_623_BC_FRAG_W_Paulina_150506_L03_ugc_623_24_F3.QV.qual >& KO_6h_replicate_II.log > KO_6h_replicate_II.fastq
/data/results/tools/adapter/cutadapt-1.9.1/bin/cutadapt -q 20 -z -m 15 -c -a CGCCTTGGCCGTACAGCAG ../Backup_Polysomes_TTP/ugc_623_BC_FRAG_W_Paulina_150506_L03_ugc_623_25_F3.csfasta /data/images/proton/DKlab/polysomes/reads/Backup_Polysomes_TTP/ugc_623_BC_FRAG_W_Paulina_150506_L03_ugc_623_25_F3.QV.qual >& KO_IL4_replicate_I.log > KO_IL4_replicate_I.fastq
/data/results/tools/adapter/cutadapt-1.9.1/bin/cutadapt -q 20 -z -m 15 -c -a CGCCTTGGCCGTACAGCAG ../Backup_Polysomes_TTP/ugc_623_BC_FRAG_W_Paulina_150506_L03_ugc_623_26_F3.csfasta /data/images/proton/DKlab/polysomes/reads/Backup_Polysomes_TTP/ugc_623_BC_FRAG_W_Paulina_150506_L03_ugc_623_26_F3.QV.qual >& KO_IL4_replicate_II.log > KO_IL4_replicate_II.fastq
/data/results/tools/adapter/cutadapt-1.9.1/bin/cutadapt -q 20 -z -m 15 -c -a CGCCTTGGCCGTACAGCAG ../Backup_Polysomes_TTP/ugc_623_BC_FRAG_W_Paulina_150506_L03_ugc_623_27_F3.csfasta /data/images/proton/DKlab/polysomes/reads/Backup_Polysomes_TTP/ugc_623_BC_FRAG_W_Paulina_150506_L03_ugc_623_27_F3.QV.qual >&  KO_IFN_replicate_I.log >  KO_IFN_replicate_I.fastq
/data/results/tools/adapter/cutadapt-1.9.1/bin/cutadapt -q 20 -z -m 15 -c -a CGCCTTGGCCGTACAGCAG ../Backup_Polysomes_TTP/ugc_623_BC_FRAG_W_Paulina_150506_L03_ugc_623_28_F3.csfasta /data/images/proton/DKlab/polysomes/reads/Backup_Polysomes_TTP/ugc_623_BC_FRAG_W_Paulina_150506_L03_ugc_623_28_F3.QV.qual >& KO_IFN-gamma_replicate_II.log > KO_IFN-gamma_replicate_II.fastq