Monthly Archives:: August 2015

A few outliers remaining

Posted by & filed under Ostrea lurida.

Integrating last bit of qPCR data into master datasheet. This includes 5 runs post 8/15. likely error above – second EF1 was 18s test. CARM Looks nice, corrected… Elong factor Correction is fine, but mechanical reps have some issues As noticed in last batch of analysis these need to be checked at raw data level… Read more »

Sifting Sands

Posted by & filed under Miscellaneous, Workflows.

Below is a quick workflow I am using to help Drinan annotate ~1.5 million sequences from an amplicon targeting NGS effort of sand. head /Users/sr320/Dropbox/hummingbird-ipython-nbs/data/DanD/meiofauna_forward_sequences.fa >M02215:33:000000000-AFA9E:1:1101:14961:2005 1:N:0:15 TGACTGTGCTAAGGTAGCATAATTAATTGTCTTTTAATTAGAGACTTGTTTGAAAGATTT TTTGAATTTAATATAGTTTTAAAATTATAAAAATGAATTTTTATATATTGGTAAAAATAC CATGATTTTTTAAAAAGACGATAAGACCCTATCAAGTTTTACTTAAATTTAAAGAAAATT TAGGTTTTAATGGGGCATTATTATTTATTTTAAATAAATTTTGATCTTAAATTAAATTTT AGGAAATTTAATAAAATTACTGTAGGGATAACAGTGTAATATTTTTTAAAGTTCATATTT A >M02215:33:000000000-AFA9E:1:1101:11050:2011 1:N:0:15 TAACTGTGCTAAGGTAGCATAATCACTTGTCTCCTAATTAGAGACTGGCATGAAAGGGTA AACTCTTTATAACTTTATAAAGCATACACACTGAAATTTTTATTTAGACGAAGAAATCTA       Within a given working directory I proceeded to (in Jupyter NB) cp meiofauna_forward_sequences.fa query.fasta –… Read more »

Finishing out with the mechanical

Posted by & filed under Ostrea lurida.

Currently there is a pretty robust spreadsheet and over the past few days Jake has cranked through some reps to see how the oysters that were mechanically stressed hold up. Below is how these data are integrated. Currently the 8-10 samples (yellow) have been skipped, but we might have a look. First up is having… Read more »

Another day, another species

Posted by & filed under Ostrea lurida.

Today we sampled Jesse, the Olympia oyster selected for genome sequencing. Not as big of a specimen as yesterday, but made up for it with video. The oyster was collected in Fidalgo Bay, weighing in at 58.99 grams and 70 mm long. The adductor muscle was selected for genome sequencing, thus quickly rinsed in 10%… Read more »

Big day, big clam

Posted by & filed under Panopea generosa.

Today we sampled the geoduck (Panopea generosa) for genome sequencing. Here is how things went down. It was an early morning for the clam, peaking out to see a glorious sunrise on the porch. From there it was off to the lab. After cleaning the surfaces, Brent sampled tissue. We started out started out targetting… Read more »

Dirty and crude with Oly qPCR

Posted by & filed under Ostrea lurida.

Taking the most decent Ct values, I did the simple and crude calculation, normalizing with EF1 and looking at fold over minimum. Seems to be EF1 data is skewing. Will take a look with actin and also compare delta Ct, using this as a sound reference.