0000-0002-2747-368X The geoduck genome assembly started 20180405 completed this weekend. This assembly utilized the BGI data and all of the Illumina project data (NMP and NovaSeq) with a kmer 101 setting. I ran Quast to gather some assembly stats, using
Data Management – SRA Submission LSU C.virginica Oil Spill MBD BS-seq Data
0000-0002-2747-368X Submitted the Crassostrea virginica (Eastern oyster) MBD BS-seq data we received on 20150413 to NCBI Sequence Read Archive. Data was uploaded via the web browser interface, as the FTP method was not functioning properly. SRA deets are below (assigned
TrimGalore/FastQC/MultiQC – Trim 10bp 5’/3′ ends C.virginica MBD BS-seq FASTQ data
0000-0002-2747-368X Steven found out that the Bismarck documentation (Bismarck is the bisulfite aligner we use in our BS-seq pipeline) suggests trimming 10bp from both the 5′ and 3′ ends. Since this is the next step in our pipeline, we figured
DNA Isolation & Quantification – Metagenomics Water Filters
0000-0002-2747-368X Isolated DNA from the following two filters: DNA was isolated with the DNeasy Blood & Tissue Kit (Qiagen), following a modified version of the Gram-Positive Bacteria protocol: filters were unfolded and unceremoniously stuffed into 1.7mL snap cap tubes did
TrimGalore/FastQC/MultiQC – 2bp 3′ end Read 1s Trim C.virginica MBD BS-seq FASTQ data
0000-0002-2747-368X Earlier today, I ran TrimGalore/FastQC/MultiQC on the Crassostrea virginica MBD BS-seq data from ZymoResearch and hard trimmed the first 14bp from each read. Things looked better at the 5′ end, but the 3′ end of each of the READ1