Comments on: Quality Trimming – LSU C.virginica Oil Spill MBD BS-Seq Data http://onsnetwork.org/kubu4/2015/04/15/quality-trimming-lsu-c-virginica-oil-spill-mbd-bs-seq-data/ University of Washington - Fishery Sciences - Roberts Lab Tue, 09 Apr 2019 18:37:58 +0000 hourly 1 http://wordpress.org/?v=4.0 By: kubu4 http://onsnetwork.org/kubu4/2015/04/15/quality-trimming-lsu-c-virginica-oil-spill-mbd-bs-seq-data/#comment-6639 Wed, 11 Apr 2018 13:43:25 +0000 http://onsnetwork.org/kubu4/?p=1260#comment-6639

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).

]]> By: kubu4 http://onsnetwork.org/kubu4/2015/04/15/quality-trimming-lsu-c-virginica-oil-spill-mbd-bs-seq-data/#comment-6636 Wed, 11 Apr 2018 02:33:05 +0000 http://onsnetwork.org/kubu4/?p=1260#comment-6636

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.

]]> By: Steven http://onsnetwork.org/kubu4/2015/04/15/quality-trimming-lsu-c-virginica-oil-spill-mbd-bs-seq-data/#comment-6635 Tue, 10 Apr 2018 23:17:05 +0000 http://onsnetwork.org/kubu4/?p=1260#comment-6635 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
“`

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