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.
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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.
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Update on Crab Pooling and Plan for next week-ish
Today I met with Steven to talk briefly about the crab sample pooling (need more info on how to proceed- will wait for Sam’s return in 1.5 weeks), and about things I can do in the interim while the samples are being sequenced: practicing Trinity with Geoduck transcriptome data; DecaPod;...
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2015 Oysterseed Skyline questions
Today I worked on trying to figure out what could have made my error rates from last week so awful. I re-did the Skyline DIA protocol many times and ended up realizing that some of my samples only had a few files listed in the protein, while others had all...
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Re-visiting error rate in Skyline and figuring out the math in pooling samples for sequencing
Today I re-did the Skyline peak-picking error rate for the 2015 Oysterseed DIA and sent off the results to Emma for feedback. I also worked on figuring out how to make the 12 pooled samples that will be sent off for sequencing. Awaiting Steven’s feedback on that.
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