Illumina GOM data – prepping for QIIME

Going through QIIME to figure out how you have to process Illumina FASTQ data – process seems like it takes a lot of prep work, especially for paired-end files. I’m using the FastX toolkit on Merlot to generate the barcode files that QIIME needs as input for demultiplexing.  Commands I ran (a whole lotta them) are as follows:

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./fastx_trimmer -Q33 -f 6 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-1_1_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-1_1_trimmed.txt

./fastx_trimmer -Q33 -f 1 -l 5 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-1_1_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-1_1_barcode.txt

./fastx_trimmer -Q33 -f 6 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-1_2_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-1_2_trimmed.txt

./fastx_trimmer -Q33 -f 1 -l 5 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-1_2_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-1_2_barcode.txt

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./fastx_trimmer -Q33 -f 6 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-2_1_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-2_1_trimmed.txt

./fastx_trimmer -Q33 -f 1 -l 5 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-2_1_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-2_1_barcode.txt

./fastx_trimmer -Q33 -f 6 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-2_2_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-2_2_trimmed.txt

./fastx_trimmer -Q33 -f 1 -l 5 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-2_2_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-2_2_barcode.txt

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./fastx_trimmer -Q33 -f 6 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-3_1_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-3_1_trimmed.txt

./fastx_trimmer -Q33 -f 1 -l 5 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-3_1_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-3_1_barcode.txt

./fastx_trimmer -Q33 -f 6 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-3_2_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-3_2_trimmed.txt

./fastx_trimmer -Q33 -f 1 -l 5 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-3_2_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-3_2_barcode.txt

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./fastx_trimmer -Q33 -f 6 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-4_1_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-4_1_trimmed.txt

./fastx_trimmer -Q33 -f 1 -l 5 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-4_1_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-4_1_barcode.txt

./fastx_trimmer -Q33 -f 6 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-4_2_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-4_2_trimmed.txt

./fastx_trimmer -Q33 -f 1 -l 5 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-4_2_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-4_2_barcode.txt

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./fastx_trimmer -Q33 -f 6 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-5_1_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-5_1_trimmed.txt

./fastx_trimmer -Q33 -f 1 -l 5 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-5_1_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-5_1_barcode.txt

./fastx_trimmer -Q33 -f 6 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-5_2_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-5_2_trimmed.txt

./fastx_trimmer -Q33 -f 1 -l 5 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-5_2_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-5_2_barcode.txt

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./fastx_trimmer -Q33 -f 6 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-6_1_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-6_1_trimmed.txt

./fastx_trimmer -Q33 -f 1 -l 5 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-6_1_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-6_1_barcode.txt

./fastx_trimmer -Q33 -f 6 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-6_2_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-6_2_trimmed.txt

./fastx_trimmer -Q33 -f 1 -l 5 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-6_2_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-6_2_barcode.txt

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./fastx_trimmer -Q33 -f 6 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-7_1_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-7_1_trimmed.txt

./fastx_trimmer -Q33 -f 1 -l 5 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-7_1_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-7_1_barcode.txt

./fastx_trimmer -Q33 -f 6 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-7_2_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-7_2_trimmed.txt

./fastx_trimmer -Q33 -f 1 -l 5 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-7_2_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-7_2_barcode.txt

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./fastx_trimmer -Q33 -f 6 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-8_1_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-8_1_trimmed.txt

./fastx_trimmer -Q33 -f 1 -l 5 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-8_1_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-8_1_barcode.txt

./fastx_trimmer -Q33 -f 6 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-8_2_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-8_2_trimmed.txt

./fastx_trimmer -Q33 -f 1 -l 5 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-8_2_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-8_2_barcode.txt

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./fastx_trimmer -Q33 -f 6 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-9_1_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-9_1_trimmed.txt

./fastx_trimmer -Q33 -f 1 -l 5 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-9_1_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-9_1_barcode.txt

./fastx_trimmer -Q33 -f 6 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-9_2_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-9_2_trimmed.txt

./fastx_trimmer -Q33 -f 1 -l 5 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-9_2_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-9_2_barcode.txt

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./fastx_trimmer -Q33 -f 6 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-10_1_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-10_1_trimmed.txt

./fastx_trimmer -Q33 -f 1 -l 5 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-10_1_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-10_1_barcode.txt

./fastx_trimmer -Q33 -f 6 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-10_2_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-10_2_trimmed.txt

./fastx_trimmer -Q33 -f 1 -l 5 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-10_2_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-10_2_barcode.txt

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./fastx_trimmer -Q33 -f 6 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-11_1_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-11_1_trimmed.txt

./fastx_trimmer -Q33 -f 1 -l 5 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-11_1_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-11_1_barcode.txt

./fastx_trimmer -Q33 -f 6 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-11_2_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-11_2_trimmed.txt

./fastx_trimmer -Q33 -f 1 -l 5 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-11_2_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-11_2_barcode.txt

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./fastx_trimmer -Q33 -f 6 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-12_1_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-12_1_trimmed.txt

./fastx_trimmer -Q33 -f 1 -l 5 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-12_1_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-12_1_barcode.txt

./fastx_trimmer -Q33 -f 6 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-12_2_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-12_2_trimmed.txt

./fastx_trimmer -Q33 -f 1 -l 5 -i /home/hbik/Illumina_GOM/raw_data/1926-KO-12_2_sequence.txt -o /home/hbik/Illumina_GOM/fastx_trimmed_files/1926-KO-12_2_barcode.txt


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