cd "/Volumes/NGS 2TB/160707_Biomass/3 cut adapt"


cutadapt -g ^ACWGGWTGRACWGTNTAYCC -o temp.txt "../2 PE read merging/BP_rerun_L001_BF10_BR14_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GCHGGDGCHATYACHATRYT$ -o BP_rerun_L001_BF10_BR14_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^ACWGGWTGRACWGTNTAYCC -o temp.txt "../2 PE read merging/BP_rerun_L001_BF10_BR24_merged.txt" -f fastq --discard-untrimmed
cutadapt -a TGRTTYTTYGGNCAYCCHGA$ -o BP_rerun_L001_BF10_BR24_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^ACWGGWTGRACWGTNTAYCC -o temp.txt "../2 PE read merging/BP_rerun_L001_BF11_BR13_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GCHGGDGCHATYACHATRYT$ -o BP_rerun_L001_BF11_BR13_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^ACWGGWTGRACWGTNTAYCC -o temp.txt "../2 PE read merging/BP_rerun_L001_BF11_BR23_merged.txt" -f fastq --discard-untrimmed
cutadapt -a TGRTTYTTYGGNCAYCCHGA$ -o BP_rerun_L001_BF11_BR23_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^ACWGGWTGRACWGTNTAYCC -o temp.txt "../2 PE read merging/BP_rerun_L001_BF12_BR12_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GCHGGDGCHATYACHATRYT$ -o BP_rerun_L001_BF12_BR12_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^ACWGGWTGRACWGTNTAYCC -o temp.txt "../2 PE read merging/BP_rerun_L001_BF12_BR22_merged.txt" -f fastq --discard-untrimmed
cutadapt -a TGRTTYTTYGGNCAYCCHGA$ -o BP_rerun_L001_BF12_BR22_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^ACWGGWTGRACWGTNTAYCC -o temp.txt "../2 PE read merging/BP_rerun_L001_BF13_BR11_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GCHGGDGCHATYACHATRYT$ -o BP_rerun_L001_BF13_BR11_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^ACWGGWTGRACWGTNTAYCC -o temp.txt "../2 PE read merging/BP_rerun_L001_BF13_BR21_merged.txt" -f fastq --discard-untrimmed
cutadapt -a TGRTTYTTYGGNCAYCCHGA$ -o BP_rerun_L001_BF13_BR21_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^ACWGGWTGRACWGTNTAYCC -o temp.txt "../2 PE read merging/BP_rerun_L001_BF14_BR10_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GCHGGDGCHATYACHATRYT$ -o BP_rerun_L001_BF14_BR10_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^ACWGGWTGRACWGTNTAYCC -o temp.txt "../2 PE read merging/BP_rerun_L001_BF14_BR20_merged.txt" -f fastq --discard-untrimmed
cutadapt -a TGRTTYTTYGGNCAYCCHGA$ -o BP_rerun_L001_BF14_BR20_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^GCHCCHGAYATRGCHTTYCC -o temp.txt "../2 PE read merging/BP_rerun_L001_BF20_BR14_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GCHGGDGCHATYACHATRYT$ -o BP_rerun_L001_BF20_BR14_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^GCHCCHGAYATRGCHTTYCC -o temp.txt "../2 PE read merging/BP_rerun_L001_BF20_BR24_merged.txt" -f fastq --discard-untrimmed
cutadapt -a TGRTTYTTYGGNCAYCCHGA$ -o BP_rerun_L001_BF20_BR24_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^GCHCCHGAYATRGCHTTYCC -o temp.txt "../2 PE read merging/BP_rerun_L001_BF21_BR13_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GCHGGDGCHATYACHATRYT$ -o BP_rerun_L001_BF21_BR13_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^GCHCCHGAYATRGCHTTYCC -o temp.txt "../2 PE read merging/BP_rerun_L001_BF21_BR23_merged.txt" -f fastq --discard-untrimmed
cutadapt -a TGRTTYTTYGGNCAYCCHGA$ -o BP_rerun_L001_BF21_BR23_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^GCHCCHGAYATRGCHTTYCC -o temp.txt "../2 PE read merging/BP_rerun_L001_BF22_BR12_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GCHGGDGCHATYACHATRYT$ -o BP_rerun_L001_BF22_BR12_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^GCHCCHGAYATRGCHTTYCC -o temp.txt "../2 PE read merging/BP_rerun_L001_BF22_BR22_merged.txt" -f fastq --discard-untrimmed
cutadapt -a TGRTTYTTYGGNCAYCCHGA$ -o BP_rerun_L001_BF22_BR22_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^GCHCCHGAYATRGCHTTYCC -o temp.txt "../2 PE read merging/BP_rerun_L001_BF23_BR11_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GCHGGDGCHATYACHATRYT$ -o BP_rerun_L001_BF23_BR11_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^GCHCCHGAYATRGCHTTYCC -o temp.txt "../2 PE read merging/BP_rerun_L001_BF23_BR21_merged.txt" -f fastq --discard-untrimmed
cutadapt -a TGRTTYTTYGGNCAYCCHGA$ -o BP_rerun_L001_BF23_BR21_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^GCHCCHGAYATRGCHTTYCC -o temp.txt "../2 PE read merging/BP_rerun_L001_BF24_BR10_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GCHGGDGCHATYACHATRYT$ -o BP_rerun_L001_BF24_BR10_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^GCHCCHGAYATRGCHTTYCC -o temp.txt "../2 PE read merging/BP_rerun_L001_BF24_BR20_merged.txt" -f fastq --discard-untrimmed
cutadapt -a TGRTTYTTYGGNCAYCCHGA$ -o BP_rerun_L001_BF24_BR20_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^ARYATDGTRATDGCHCCDGC -o temp.txt "../2 PE read merging/BP_rerun_L001_BR10_BF14_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GGRTANACWGTYCAWCCWGT$ -o BP_rerun_L001_BR10_BF14_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^ARYATDGTRATDGCHCCDGC -o temp.txt "../2 PE read merging/BP_rerun_L001_BR10_BF24_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GGRAADGCYATRTCDGGDGC$ -o BP_rerun_L001_BR10_BF24_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^ARYATDGTRATDGCHCCDGC -o temp.txt "../2 PE read merging/BP_rerun_L001_BR11_BF13_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GGRTANACWGTYCAWCCWGT$ -o BP_rerun_L001_BR11_BF13_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^ARYATDGTRATDGCHCCDGC -o temp.txt "../2 PE read merging/BP_rerun_L001_BR11_BF23_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GGRAADGCYATRTCDGGDGC$ -o BP_rerun_L001_BR11_BF23_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^ARYATDGTRATDGCHCCDGC -o temp.txt "../2 PE read merging/BP_rerun_L001_BR12_BF12_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GGRTANACWGTYCAWCCWGT$ -o BP_rerun_L001_BR12_BF12_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^ARYATDGTRATDGCHCCDGC -o temp.txt "../2 PE read merging/BP_rerun_L001_BR12_BF22_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GGRAADGCYATRTCDGGDGC$ -o BP_rerun_L001_BR12_BF22_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^ARYATDGTRATDGCHCCDGC -o temp.txt "../2 PE read merging/BP_rerun_L001_BR13_BF11_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GGRTANACWGTYCAWCCWGT$ -o BP_rerun_L001_BR13_BF11_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^ARYATDGTRATDGCHCCDGC -o temp.txt "../2 PE read merging/BP_rerun_L001_BR13_BF21_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GGRAADGCYATRTCDGGDGC$ -o BP_rerun_L001_BR13_BF21_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^ARYATDGTRATDGCHCCDGC -o temp.txt "../2 PE read merging/BP_rerun_L001_BR14_BF10_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GGRTANACWGTYCAWCCWGT$ -o BP_rerun_L001_BR14_BF10_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^ARYATDGTRATDGCHCCDGC -o temp.txt "../2 PE read merging/BP_rerun_L001_BR14_BF20_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GGRAADGCYATRTCDGGDGC$ -o BP_rerun_L001_BR14_BF20_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^TCDGGRTGNCCRAARAAYCA -o temp.txt "../2 PE read merging/BP_rerun_L001_BR20_BF14_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GGRTANACWGTYCAWCCWGT$ -o BP_rerun_L001_BR20_BF14_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^TCDGGRTGNCCRAARAAYCA -o temp.txt "../2 PE read merging/BP_rerun_L001_BR20_BF24_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GGRAADGCYATRTCDGGDGC$ -o BP_rerun_L001_BR20_BF24_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^TCDGGRTGNCCRAARAAYCA -o temp.txt "../2 PE read merging/BP_rerun_L001_BR21_BF13_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GGRTANACWGTYCAWCCWGT$ -o BP_rerun_L001_BR21_BF13_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^TCDGGRTGNCCRAARAAYCA -o temp.txt "../2 PE read merging/BP_rerun_L001_BR21_BF23_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GGRAADGCYATRTCDGGDGC$ -o BP_rerun_L001_BR21_BF23_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^TCDGGRTGNCCRAARAAYCA -o temp.txt "../2 PE read merging/BP_rerun_L001_BR22_BF12_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GGRTANACWGTYCAWCCWGT$ -o BP_rerun_L001_BR22_BF12_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^TCDGGRTGNCCRAARAAYCA -o temp.txt "../2 PE read merging/BP_rerun_L001_BR22_BF22_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GGRAADGCYATRTCDGGDGC$ -o BP_rerun_L001_BR22_BF22_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^TCDGGRTGNCCRAARAAYCA -o temp.txt "../2 PE read merging/BP_rerun_L001_BR23_BF11_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GGRTANACWGTYCAWCCWGT$ -o BP_rerun_L001_BR23_BF11_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^TCDGGRTGNCCRAARAAYCA -o temp.txt "../2 PE read merging/BP_rerun_L001_BR23_BF21_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GGRAADGCYATRTCDGGDGC$ -o BP_rerun_L001_BR23_BF21_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^TCDGGRTGNCCRAARAAYCA -o temp.txt "../2 PE read merging/BP_rerun_L001_BR24_BF10_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GGRTANACWGTYCAWCCWGT$ -o BP_rerun_L001_BR24_BF10_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^TCDGGRTGNCCRAARAAYCA -o temp.txt "../2 PE read merging/BP_rerun_L001_BR24_BF20_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GGRAADGCYATRTCDGGDGC$ -o BP_rerun_L001_BR24_BF20_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^ACWGGWTGRACWGTNTAYCC -o temp.txt "../2 PE read merging/BP_rerun_L002_BF10_BR14_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GCHGGDGCHATYACHATRYT$ -o BP_rerun_L002_BF10_BR14_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^ACWGGWTGRACWGTNTAYCC -o temp.txt "../2 PE read merging/BP_rerun_L002_BF10_BR24_merged.txt" -f fastq --discard-untrimmed
cutadapt -a TGRTTYTTYGGNCAYCCHGA$ -o BP_rerun_L002_BF10_BR24_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^ACWGGWTGRACWGTNTAYCC -o temp.txt "../2 PE read merging/BP_rerun_L002_BF11_BR13_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GCHGGDGCHATYACHATRYT$ -o BP_rerun_L002_BF11_BR13_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^ACWGGWTGRACWGTNTAYCC -o temp.txt "../2 PE read merging/BP_rerun_L002_BF11_BR23_merged.txt" -f fastq --discard-untrimmed
cutadapt -a TGRTTYTTYGGNCAYCCHGA$ -o BP_rerun_L002_BF11_BR23_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^ACWGGWTGRACWGTNTAYCC -o temp.txt "../2 PE read merging/BP_rerun_L002_BF12_BR12_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GCHGGDGCHATYACHATRYT$ -o BP_rerun_L002_BF12_BR12_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^ACWGGWTGRACWGTNTAYCC -o temp.txt "../2 PE read merging/BP_rerun_L002_BF12_BR22_merged.txt" -f fastq --discard-untrimmed
cutadapt -a TGRTTYTTYGGNCAYCCHGA$ -o BP_rerun_L002_BF12_BR22_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^ACWGGWTGRACWGTNTAYCC -o temp.txt "../2 PE read merging/BP_rerun_L002_BF13_BR11_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GCHGGDGCHATYACHATRYT$ -o BP_rerun_L002_BF13_BR11_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^ACWGGWTGRACWGTNTAYCC -o temp.txt "../2 PE read merging/BP_rerun_L002_BF13_BR21_merged.txt" -f fastq --discard-untrimmed
cutadapt -a TGRTTYTTYGGNCAYCCHGA$ -o BP_rerun_L002_BF13_BR21_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^ACWGGWTGRACWGTNTAYCC -o temp.txt "../2 PE read merging/BP_rerun_L002_BF14_BR10_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GCHGGDGCHATYACHATRYT$ -o BP_rerun_L002_BF14_BR10_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^ACWGGWTGRACWGTNTAYCC -o temp.txt "../2 PE read merging/BP_rerun_L002_BF14_BR20_merged.txt" -f fastq --discard-untrimmed
cutadapt -a TGRTTYTTYGGNCAYCCHGA$ -o BP_rerun_L002_BF14_BR20_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^GCHCCHGAYATRGCHTTYCC -o temp.txt "../2 PE read merging/BP_rerun_L002_BF20_BR14_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GCHGGDGCHATYACHATRYT$ -o BP_rerun_L002_BF20_BR14_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^GCHCCHGAYATRGCHTTYCC -o temp.txt "../2 PE read merging/BP_rerun_L002_BF20_BR24_merged.txt" -f fastq --discard-untrimmed
cutadapt -a TGRTTYTTYGGNCAYCCHGA$ -o BP_rerun_L002_BF20_BR24_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^GCHCCHGAYATRGCHTTYCC -o temp.txt "../2 PE read merging/BP_rerun_L002_BF21_BR13_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GCHGGDGCHATYACHATRYT$ -o BP_rerun_L002_BF21_BR13_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^GCHCCHGAYATRGCHTTYCC -o temp.txt "../2 PE read merging/BP_rerun_L002_BF21_BR23_merged.txt" -f fastq --discard-untrimmed
cutadapt -a TGRTTYTTYGGNCAYCCHGA$ -o BP_rerun_L002_BF21_BR23_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^GCHCCHGAYATRGCHTTYCC -o temp.txt "../2 PE read merging/BP_rerun_L002_BF22_BR12_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GCHGGDGCHATYACHATRYT$ -o BP_rerun_L002_BF22_BR12_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^GCHCCHGAYATRGCHTTYCC -o temp.txt "../2 PE read merging/BP_rerun_L002_BF22_BR22_merged.txt" -f fastq --discard-untrimmed
cutadapt -a TGRTTYTTYGGNCAYCCHGA$ -o BP_rerun_L002_BF22_BR22_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^GCHCCHGAYATRGCHTTYCC -o temp.txt "../2 PE read merging/BP_rerun_L002_BF23_BR11_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GCHGGDGCHATYACHATRYT$ -o BP_rerun_L002_BF23_BR11_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^GCHCCHGAYATRGCHTTYCC -o temp.txt "../2 PE read merging/BP_rerun_L002_BF23_BR21_merged.txt" -f fastq --discard-untrimmed
cutadapt -a TGRTTYTTYGGNCAYCCHGA$ -o BP_rerun_L002_BF23_BR21_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^GCHCCHGAYATRGCHTTYCC -o temp.txt "../2 PE read merging/BP_rerun_L002_BF24_BR10_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GCHGGDGCHATYACHATRYT$ -o BP_rerun_L002_BF24_BR10_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^GCHCCHGAYATRGCHTTYCC -o temp.txt "../2 PE read merging/BP_rerun_L002_BF24_BR20_merged.txt" -f fastq --discard-untrimmed
cutadapt -a TGRTTYTTYGGNCAYCCHGA$ -o BP_rerun_L002_BF24_BR20_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^ARYATDGTRATDGCHCCDGC -o temp.txt "../2 PE read merging/BP_rerun_L002_BR10_BF14_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GGRTANACWGTYCAWCCWGT$ -o BP_rerun_L002_BR10_BF14_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^ARYATDGTRATDGCHCCDGC -o temp.txt "../2 PE read merging/BP_rerun_L002_BR10_BF24_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GGRAADGCYATRTCDGGDGC$ -o BP_rerun_L002_BR10_BF24_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^ARYATDGTRATDGCHCCDGC -o temp.txt "../2 PE read merging/BP_rerun_L002_BR11_BF13_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GGRTANACWGTYCAWCCWGT$ -o BP_rerun_L002_BR11_BF13_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^ARYATDGTRATDGCHCCDGC -o temp.txt "../2 PE read merging/BP_rerun_L002_BR11_BF23_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GGRAADGCYATRTCDGGDGC$ -o BP_rerun_L002_BR11_BF23_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^ARYATDGTRATDGCHCCDGC -o temp.txt "../2 PE read merging/BP_rerun_L002_BR12_BF12_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GGRTANACWGTYCAWCCWGT$ -o BP_rerun_L002_BR12_BF12_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^ARYATDGTRATDGCHCCDGC -o temp.txt "../2 PE read merging/BP_rerun_L002_BR12_BF22_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GGRAADGCYATRTCDGGDGC$ -o BP_rerun_L002_BR12_BF22_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^ARYATDGTRATDGCHCCDGC -o temp.txt "../2 PE read merging/BP_rerun_L002_BR13_BF11_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GGRTANACWGTYCAWCCWGT$ -o BP_rerun_L002_BR13_BF11_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^ARYATDGTRATDGCHCCDGC -o temp.txt "../2 PE read merging/BP_rerun_L002_BR13_BF21_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GGRAADGCYATRTCDGGDGC$ -o BP_rerun_L002_BR13_BF21_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^ARYATDGTRATDGCHCCDGC -o temp.txt "../2 PE read merging/BP_rerun_L002_BR14_BF10_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GGRTANACWGTYCAWCCWGT$ -o BP_rerun_L002_BR14_BF10_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^ARYATDGTRATDGCHCCDGC -o temp.txt "../2 PE read merging/BP_rerun_L002_BR14_BF20_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GGRAADGCYATRTCDGGDGC$ -o BP_rerun_L002_BR14_BF20_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^TCDGGRTGNCCRAARAAYCA -o temp.txt "../2 PE read merging/BP_rerun_L002_BR20_BF14_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GGRTANACWGTYCAWCCWGT$ -o BP_rerun_L002_BR20_BF14_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^TCDGGRTGNCCRAARAAYCA -o temp.txt "../2 PE read merging/BP_rerun_L002_BR20_BF24_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GGRAADGCYATRTCDGGDGC$ -o BP_rerun_L002_BR20_BF24_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^TCDGGRTGNCCRAARAAYCA -o temp.txt "../2 PE read merging/BP_rerun_L002_BR21_BF13_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GGRTANACWGTYCAWCCWGT$ -o BP_rerun_L002_BR21_BF13_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^TCDGGRTGNCCRAARAAYCA -o temp.txt "../2 PE read merging/BP_rerun_L002_BR21_BF23_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GGRAADGCYATRTCDGGDGC$ -o BP_rerun_L002_BR21_BF23_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^TCDGGRTGNCCRAARAAYCA -o temp.txt "../2 PE read merging/BP_rerun_L002_BR22_BF12_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GGRTANACWGTYCAWCCWGT$ -o BP_rerun_L002_BR22_BF12_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^TCDGGRTGNCCRAARAAYCA -o temp.txt "../2 PE read merging/BP_rerun_L002_BR22_BF22_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GGRAADGCYATRTCDGGDGC$ -o BP_rerun_L002_BR22_BF22_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^TCDGGRTGNCCRAARAAYCA -o temp.txt "../2 PE read merging/BP_rerun_L002_BR23_BF11_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GGRTANACWGTYCAWCCWGT$ -o BP_rerun_L002_BR23_BF11_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^TCDGGRTGNCCRAARAAYCA -o temp.txt "../2 PE read merging/BP_rerun_L002_BR23_BF21_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GGRAADGCYATRTCDGGDGC$ -o BP_rerun_L002_BR23_BF21_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^TCDGGRTGNCCRAARAAYCA -o temp.txt "../2 PE read merging/BP_rerun_L002_BR24_BF10_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GGRTANACWGTYCAWCCWGT$ -o BP_rerun_L002_BR24_BF10_merged_cut.txt temp.txt -f fastq --discard-untrimmed

cutadapt -g ^TCDGGRTGNCCRAARAAYCA -o temp.txt "../2 PE read merging/BP_rerun_L002_BR24_BF20_merged.txt" -f fastq --discard-untrimmed
cutadapt -a GGRAADGCYATRTCDGGDGC$ -o BP_rerun_L002_BR24_BF20_merged_cut.txt temp.txt -f fastq --discard-untrimmed

