Today we had our 4th crab meeting and discussed our short-term sequencing plan for 3 libraries (1: day 9 uninfected; 2: day 9 infected; and 3:a “masterpool” from the reamining 10 treatments). We also discussed our plan going forward with qPCR and creating libraries later and we hopefully will see...
[Read More]
New Crab Pooling Plan for RNA Seq
Today I met with Sam and Steven a couple times to figure out what we’re going to discuss this Thursday with Pam. Steven and Sam have come up with three pools that we feel are a good place to start because unfortunately there’s not enough RNA to do the original...
[Read More]
Learning more about Trinity and working with large data sets; Update on Skyline issue
Today I read more about using Trinity and functional genomics as well as got some information back from Nick from Skyline in regards to my high error rate in peak-picking.
[Read More]
Reading up on Trinity and Interviewed Genevieve Johnson for DecaPod
Today I did more reading on how to start assembling a transcriptome using Trinity with plans to formulate the beginning steps tomorrow and I interviewed Genevieve Johnson (University of Alaska, Fairbanks) on her thesis project doing Tanner Crab population genetics for a new soon-to-be published episode of DecaPod.
[Read More]
Still have high error rates in Skyline - posted my issue to the Skyline support page
Today I went through all my setting and files in Skyline for the 2015Oysterseed proteomic project and re-did my Skyline Daily peak-picking error rate determination. I still got an error rate nearing 50%, so per Emma’s suggestion, I submitted the issue to Skyline’s support page.
[Read More]