Site-Wide Activity

Sam White wrote a new post, Kmer Estimation – Kmergenie on Geoduck Sequence Data (default settings), on the site Sam's Notebook 2 days, 5 hours ago

After the last SparseAssembler assembly completed, I wanted to do another run with a different kmer size (last time was arbitrarily set at 101). However, I didn’t really know how to decide, particularly since this […]
Sam White wrote a new post, Assembly Stats – Quast Stats for Geoduck SparseAssembler Job from 20180405, on the site Sam's Notebook 6 days, 5 hours ago

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 […]
Sam White wrote a new post, Data Management – SRA Submission LSU C.virginica Oil Spill MBD BS-seq Data, on the site Sam's Notebook 1 week, 2 days ago

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 […]
Sam White wrote a new post, TrimGalore/FastQC/MultiQC – Trim 10bp 5’/3′ ends C.virginica MBD BS-seq FASTQ data, on the site Sam's Notebook 1 week, 3 days ago

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, […]
Sam White wrote a new post, DNA Isolation & Quantification – Metagenomics Water Filters, on the site Sam's Notebook 1 week, 3 days ago
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 […]
Sam White wrote a new post, TrimGalore/FastQC/MultiQC – 14bp Trim C.virginica MBD BS-seq FASTQ data, on the site Sam's Notebook 1 week, 4 days ago

Yesterday, I ran TrimGalore/FastQC/MultiQC on the Crassostrea virginica MBD BS-seq data from ZymoResearch with the default settings (i.e. “auto-trim”). There was still some variability in the first ~15bp of the […]
Sam White wrote a new post, TrimGalore/FastQC/MultiQC – 2bp 3′ end Read 1s Trim C.virginica MBD BS-seq FASTQ data, on the site Sam's Notebook 1 week, 4 days ago

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 […]
Sam White wrote a new post, TrimGalore/FastQC/MultiQC – Auto-trim C.virginica MBD BS-seq FASTQ data, on the site Sam's Notebook 1 week, 5 days ago

Yesterday, I ran FastQC/MultiQC on the Crassostrea virginica MBD BS-seq data from ZymoResearch. Steven wanted to trim it and see how things turned out.

I ran TrimGalore (using the built-in FastQC option) and […]
Sam White wrote a new post, FastQC/MultiQC – C. virginica MBD BS-seq Data, on the site Sam's Notebook 1 week, 5 days ago

Per Steven’s GitHub Issues request, I ran FastQC on the Eastern oyster MBD bisulfite sequencing data we recently got back from ZymoResearch.

Ran FastQC locally with the following script: <a […]
Sam White wrote a new post, Genome Assembly – SparseAssembler Geoduck Genomic Data, kmer=101, on the site Sam's Notebook 2 weeks, 2 days ago

UPDATE 20180413

Assembly complete. See end of post for data locations.

UPDATE 20180410

Received a status update email:

SLURM Job_id=156637 Name=20180405_sparse_assembler_kmer101_geo Ended, Run time […]
Sam White wrote a new post, Gunzip – BGI HiSeq Geoduck Genome Sequencing Data , on the site Sam's Notebook 2 weeks, 2 days ago
In preparation to run SpareAssembler, I needed to gunzip the BGI gzipped FASTQ files from 20180327.

Ran the following slurm script on our Mox node:
```
#!/bin/bash
## Job Name
#SBATCH […]
```
Jay Dimond wrote a new post, More RNA extractions, on the site Jay's lab notebook 2 weeks, 2 days ago

Continued RNA extractions of Anthopleura elegantissima samples using the Qiagen RNeasy kit. Further information on these samples can be found in this post. Qiashredder columns were again used for sample […]
Sam White wrote a new post, Gunzip – Trimmed Illumina Geoduck HiSeq Genome Sequencing Data , on the site Sam's Notebook 2 weeks, 3 days ago
In preparation to run SpareAssembler, I needed to gunzip the trimmed gzipped FASTQ files from 20140401.

Ran the following slurm script on our Mox node:
```
#!/bin/bash
## Job Name
#SBATCH […]
```
Sam White wrote a new post, DNA Isolation & Quantification – Geoduck larvae metagenome filter rinses, on the site Sam's Notebook 2 weeks, 4 days ago

This is another attempt to isolate DNA from two more of the geoduck hatchery metagenome samples Emma delivered on 20180313.

The previous attempt, using DNAzol, did not yield any DNA.

I isolated DNA from the […]
Sam White wrote a new post, Titrations – Yaamini’s Seawater Samples, on the site Sam's Notebook 2 weeks, 4 days ago
All data is deposited in the following GitHub repo:
- RobertsLab/titrator
Sample sizes: ~50g

LabX Method:
- pH_TA_titration.pdf
Daily pH calibration data file:
- <a […]
Sam White wrote a new post, Titrations – Yaamini’s Seawater Samples, on the site Sam's Notebook 2 weeks, 5 days ago
All data is deposited in the following GitHub repo:
- RobertsLab/titrator
Sample sizes: ~50g

LabX Methods:
- TA_titration.pdf
- pH_TA_titration.pdf
Daily pH calibration data file:
- <a […]
Sam White wrote a new post, TrimGalore!/FastQC/MultiQC – Illumina HiSeq Genome Sequencing Data Continued, on the site Sam's Notebook 2 weeks, 6 days ago

The previous attempt at this was interrupted by a random glitch with our Mox HPC node.

I removed the last files processed by TrimGalore!, just in case they were incomplete. I updated the slurm script to process […]
Sam White wrote a new post, Data Received – Crassostrea virginica MBD BS-seq from ZymoResearch, on the site Sam's Notebook 3 weeks, 2 days ago

Received the sequencing data from ZymoResearch for the <em>Crassostrea virginica</em> gonad MBD DNA that was sent to them on 20180207 for bisulfite conversion, library construction, and sequencing.

Gzipped FASTQ […]
Jay Dimond wrote a new post, RNA extraction – coral and anemone samples, on the site Jay's lab notebook 3 weeks, 3 days ago

I did some further RNA extractions of Porites astreoides and Anthopleura elegantissima samples using the Qiagen RNeasy kit. Further information on these samples can be found in the previous post. I again used […]
Sam White wrote a new post, FastQC/MultiQC – Illumina HiSeq Genome Sequencing Data, on the site Sam's Notebook 3 weeks, 3 days ago

Since running SparseAssembler seems to be working and actually able to produce assemblies, I’ve decided I’ll try to beef up the geoduck genome assembly with the rest of our existing genomic sequencing data.

<a […]
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