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

Jupyter (IPython) Notebook: 20150414_C_virginica_LSU_Oil_Spill_Trimmomatic_FASTQC.ipynb

### Trimmed FASTQC

#### HB30 25,000ppm oil Index – TGACCA

20150414_trimmed_2112_lane1_TGACCA_L001_R1_001_fastqc.html

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. Steven says:

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).