Tag Archives: GenBank

Data Management – SRA Submission LSU C.virginica Oil Spill MBD BS-seq Data

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 FASTQ files to new BioProject and created new BioSamples).

SRA Study: SRP139854
BioProject: PRJNA449904

BioSamples Table

Sample Treatment BioSample
HB2 oil 25,000ppm SAMN08919868
HB16 oil 25,000ppm SAMN08919921
HB30 oil 25,000ppm SAMN08919953
NB3 unexposed SAMN08919461
NB6 unexposed SAMN08919577
NB11 unexposed SAMN08919772

BLAST – C.gigas Larvae OA Illumina Data Against GenBank nt DB

In an attempt to figure out what’s going on with the Illumina data we recently received for these samples, I BLASTed the 400ppm data set that had previously been de-novo assembled by Steven: EmmaBS400.fa.

Jupyter (IPython) Notebook : 20150501_Cgigas_larvae_OA_BLASTn_nt.ipynb

Notebook Viewer : 20150501_Cgigas_larvae_OA_BLASTn_nt


BLASTn Output File: 20150501_nt_blastn.tab

BLAST e-vals <= 0.001: 20150501_Cgigas_larvae_OA_blastn_evals_0.001.txt

Unique BLAST Species: 20150501_Cgigas_larvae_OA_unique_blastn_evals.txt


Firstly, since this library was bisulfite converted, we know that matching won’t be as robust as we’d normally see.

However, the BLAST matches for this are terrible.

Only 0.65% of the BLAST matches (e-value <0.001) are to Crassostrea gigas. Yep, you read that correctly: 0.65%.

It’s nearly 40-fold less than the top species: Dictyostelium discoideum (a slime mold)

It’s 30-fold less than the next species: Danio rerio (zebra fish)

Then it’s followed up by human and mouse.

I think I will need to contact the Univ. of Oregon sequencing facility to see what their thoughts on this data is, because it’s not even remotely close to what we should be seeing, even with the bisulfite conversion…