Posts Categorized: Miscellaneous

The Little Things

Posted by & filed under Miscellaneous.

Getting back into gear, I am assisting Andrew ID some targets from a salmonid transcriptome. With said transcriptome I am taking the blast output and getting some protein names sans SQLshare. The tldr can be seen here, but if you have the time I will point out the key code aspects and leave you with… Read more »

Bringing Ocean Acidification System online

Posted by & filed under Miscellaneous.

I was out at Manchester yesterday to help Laura out with getting things going. tldr- Water is flowing, rising temperature seems to be an issue. This could be attributed to air temp and/or pumps. When we arrived water temperature was up to 19C after about a week. We decided to drain down system refill, calibrate… 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 »