Sean’s Notebook: Things went from…

Sean’s Notebook: Things went from not working, to working. It’s a miracle!

So I’d been having problems with Platanus throwing a segmentation fault during graph construction with a smaller k-mer length argument, which was a pain because it’s such a generic error. Turns out it just needed more memory, because 400gb isn’t enough? Hopefully it will be done by tomorrow and we can get try Redundans again, with better results!

Also, I got MethylExtract working on the C. virginica methylation data. Looks like when you have PBAT data, you have to switch the flags to flagW=0 and flagC=16, even though you’re using paired end data.

MethylExtract notebook: here
C. virginia CG and SNP data: here pending renaming/reorganization of files.

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