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Roberts Lab Documents
http://sr320.github.io/LabDocs/
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Determine Geoduck Illumina Data status #658

Closed sr320 closed 6 years ago

kubu4 commented 6 years ago

Hi Sam, Thanks for checking in. I found out from Jon that in checking the data from the first run on the NovaSeq that we had conflicting indexes between the MP libraries and a couple of the RNASeq libraries. That meant we could not de-convolute some of the RNA output from the MP output. A bit of a “genome in a box” unanticipated “good to know”. This means we had to redo the NovaSeq run after removing a couple of the RNASeq libraries. I don’t have details on which of the RNAseq samples needed to be removed and am cc’ing Jon on this. I talked to Jon yesterday and he is transferring data and can update us once it is ready to ship out. So sorry for the delay (I am saying that a lot to you and for that I apologize). I am still working on the 10x library effort and will let you know when and if I have some traction there. Cindy

kubu4 commented 6 years ago

My very rough notes from meeting w/Cindy and Jon:

Sequencing saturates diversity of libraries

No paired-end libraries.

Coverage depends on diversity of of mate-pair libraries.

Different sizes of mate pair libraries.

More DNA needed for 10x sequencing.

HDD structure:

HiSeq - mate pair and RNAseq MiSeq - RNAseq NovaSeq - RNAseq and mate pair? (mention of index collision)

kubu4 commented 6 years ago

Cindy's recap from meeting:

Hello all, Thank you so much for your HiSeq folders for RNASeq and Mate Pair libraries NovaSeq run for all combined. The MP libraries have a 800 bp insert and the RNA Seq libraries have a 300bp insert so they were loaded in a 10:1 MP:RNA into the NovaSeq. There is a sample sheet loaded on the hard drive that should indicate sample identifiers. Those identifiers are in the sequence files. Next steps: Cindy to reach out to 10xGenomics regarding how to complete the geoduck sequencing project with a 10xG library. Recommended kit from 10x is a magnetic bead kit that I will get details for. Next run we plan to include all preps (MP, RNASeq, 10xG) into a single run. Sam to have a look at data, follow up with questions and share any interesting observations. Let’s plan to get this into a coherent story by PAG 2018. C Cindy Taylor Lawley, PhD