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
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.
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
“`
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).