GOM re-de-multiplexing and looking at PhyloSift sprint issues

GAH!!! My GOM demultiplexing attempt #2 failed horribly–forgot to change the Mapping files for each barcode, so ended up with the same (incorrect) sample labels across all files. Re-de-multiplexing now with the corrected commands:

split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-2_1_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-2_1_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_2_1/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_2.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20

split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-2_2_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-2_2_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_2_2/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_2.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20
split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-3_1_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-3_1_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_3_1/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_3.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20

split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-3_2_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-3_2_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_3_2/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_3.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20
split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-4_1_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-4_1_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_4_1/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_4.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20

split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-4_2_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-4_2_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_4_2/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_4.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20
split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-5_1_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-5_1_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_5_1/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_5.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20

split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-5_2_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-5_2_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_5_2/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_5.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20
split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-6_1_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-6_1_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_6_1/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_6.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20

split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-6_2_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-6_2_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_6_2/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_6.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20
split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-7_1_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-7_1_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_7_1/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_7.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20

split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-7_2_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-7_2_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_7_2/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_7.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20
split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-8_1_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-8_1_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_8_1/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_8.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20

split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-8_2_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-8_2_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_8_2/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_8.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20
split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-9_1_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-9_1_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_9_1/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_9.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20

split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-9_2_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-9_2_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_9_2/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_9.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20
split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-10_1_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-10_1_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_10_1/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_10.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20

split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-10_2_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-10_2_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_10_2/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_10.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20
split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-11_1_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-11_1_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_11_1/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_11.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20

split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-11_2_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-11_2_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_11_2/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_11.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20
split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-12_1_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-12_1_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_12_1/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_12.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20

split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-12_2_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-12_2_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_12_2/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_12.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20

PhyloSift stuff I did today:

  • Closed issue for updating website with dynamic FASTQ quality trimming info
  • Investigated build_marker some more. Seems like read conciler doesn’t like 2 sequences or less in a file, so you have to generate a taxon map manually (which I did — running a test of the new xeno marker set with taxon map to see if I can get any results from raw Illumina data. Command ran: ./phylosift.pl all ~/Desktop/PhyloSift/test_data/xeno_unassembled/xeno_raw_s_2_1_sequence.txt (on iMac). Build_marker fix may need to be hard coded eventually…esp. if users only have a few sequences and want to use it.
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