Posts By: Steven Roberts

Data check on Oly BS-Seq samples

Posted by & filed under Ostrea lurida.

  For the 12 samples Select 4 samples from 1NF gel take 2 Select 4 samples from 2NF gel take 2 Select 2 from gel take 2 Lotterhos M1 M2 M3 Select 2 from the following sent to Katie (do not have to run on gel) NF2 14 NF2 6 NF2 18 NF2 15 NF2… Read more »

From Ensenada and beyond

Posted by & filed under Panopea generosa.

There have not been many posts recently, but that is not to say I have not been doing any science. Much of what I have been doing is numerous burst commits on the Panopea transcriptome paper / project. This can be found @ https://github.com/sr320/paper-pano-go. You can see all the Jupyter nbs in this sub-directory. I… Read more »

Using ESearch and EFetch to retrieve data

Posted by & filed under Tutorial.

Lets say there was this person, we will call her Emma for now, that needed to download lots of data but wanted to make it more robust and reliable. Here is a way to use NCBI ESearch and EFetch tools to do so. Complete documention at http://www.ncbi.nlm.nih.gov/books/NBK25498/. Specific example used is here Example one: Download… Read more »

Running the numbers

Posted by & filed under Ostrea lurida.

Today I brought another 16 samples into the DNA extraction pipeline. These were subjected to 30 minute ProK digestion at 60C as opposed to overnight. It became clear the number scheme was complicated thus I converted to 1-32. Will keep this running fwd and cross-referencing. In the future the number scheme will be simpler, but… Read more »

Upon improving extractions

Posted by & filed under Ostrea lurida.

In an attempt to determine most efficient means to get some high quality DNA from the archived oyster samples – a suite of samples were started out with M1 buffer and ProK. The first ‘unit’ to go through will be the April Dabob samples. For today, I took 16 samples from the Hood canal population… Read more »

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 »