Quality Trimming – LSU C.virginica Oil Spill MBD BS-Seq Data

Jupyter (IPython) Notebook: 20150414_C_virginica_LSU_Oil_Spill_Trimmomatic_FASTQC.ipynb

NBviewer: 20150414_C_virginica_LSU_Oil_Spill_Trimmomatic_FASTQC.ipynb

Trimmed FASTQC

NB3 No oil Index – ACAGTG

20150414_trimmed_2112_lane1_ACAGTG_L001_R1_001_fastqc.html
20150414_trimmed_2112_lane1_ACAGTG_L001_R1_002_fastqc.html

NB6 No oil Index – GCCAAT

20150414_trimmed_2112_lane1_GCCAAT_L001_R1_001_fastqc.html
20150414_trimmed_2112_lane1_GCCAAT_L001_R1_002_fastqc.html

NB11 No oil Index – CAGATC

20150414_trimmed_2112_lane1_CAGATC_L001_R1_001_fastqc.html
20150414_trimmed_2112_lane1_CAGATC_L001_R1_002_fastqc.html
20150414_trimmed_2112_lane1_CAGATC_L001_R1_003_fastqc.html

HB2 25,000ppm oil Index – ATCACG

20150414_trimmed_2112_lane1_ATCACG_L001_R1_001_fastqc.html
20150414_trimmed_2112_lane1_ATCACG_L001_R1_002_fastqc.html
20150414_trimmed_2112_lane1_ATCACG_L001_R1_003_fastqc.html

HB16 25,000ppm oil Index – TTAGGC

20150414_trimmed_2112_lane1_TTAGGC_L001_R1_001_fastqc.html
20150414_trimmed_2112_lane1_TTAGGC_L001_R1_002_fastqc.html

HB30 25,000ppm oil Index – TGACCA

20150414_trimmed_2112_lane1_TGACCA_L001_R1_001_fastqc.html

3 comments

  1. Looks like they don’t live anywhere. Very strange. They’ll need to be re-trimmed.

    However, a bigger concern I stumbled across is that the all of the raw 2212_lane2 reads aren’t in nightingales!

    I’ll copy over the 2212_lane2 reads shortly.

  2. Where do these trimmed files live?

    Some but not all are at
    ls /Volumes/web/Arabidopsis/20150414_trimmed_2212*.fastq.gz

    “`
    /Volumes/web/Arabidopsis/20150414_trimmed_2212_lane2_1000ppm_CTTGTA.fastq.gz
    /Volumes/web/Arabidopsis/20150414_trimmed_2212_lane2_400ppm_GCCAAT.fastq.gz
    /Volumes/web/Arabidopsis/20150414_trimmed_2212_lane2_CTTGTA_L002_R1_001.fastq.gz
    /Volumes/web/Arabidopsis/20150414_trimmed_2212_lane2_CTTGTA_L002_R1_002.fastq.gz
    /Volumes/web/Arabidopsis/20150414_trimmed_2212_lane2_CTTGTA_L002_R1_003.fastq.gz
    /Volumes/web/Arabidopsis/20150414_trimmed_2212_lane2_CTTGTA_L002_R1_004.fastq.gz
    /Volumes/web/Arabidopsis/20150414_trimmed_2212_lane2_GCCAAT_L002_R1_001.fastq.gz
    /Volumes/web/Arabidopsis/20150414_trimmed_2212_lane2_GCCAAT_L002_R1_002.fastq.gz
    /Volumes/web/Arabidopsis/20150414_trimmed_2212_lane2_GCCAAT_L002_R1_003.fastq.gz
    /Volumes/web/Arabidopsis/20150414_trimmed_2212_lane2_GCCAAT_L002_R1_004.fastq.gz
    /Volumes/web/Arabidopsis/20150414_trimmed_2212_lane2_GCCAAT_L002_R1_005.fastq.gz
    /Volumes/web/Arabidopsis/20150414_trimmed_2212_lane2_GCCAAT_L002_R1_006.fastq.gz
    “`

    1. Sorry! I got confused about this. I was looking at the 2112 sequences because your comment is in a notebook about C.virginica data (2112 sequences).

      However, the files you listed in your comment are the 2212 set and those are C.gigas.

      Did you mean to ask about the C.gigas files? If yes, those are all of the files (i.e. there aren’t any missing).

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