Lots of moving files and output stuff:

I pushed a bunch of files up to Owl from things I’ve been doing the past week, so here’s links!

Dammit output for Marcos’ Strand specific fine flounder RNA-Seq assembly: here.

Bismark output for C .virginica methylation data, with ambiguous and unmapped reads here. Interesting because of how much more data is unmapped compared to ambiguous or mapped. I’m experimenting with different seed lengths to hopefully increase mapping rates with Bismark, or at least see how it changes the output.

SRA Downloads finally finished! I went through and checked and things look to have downloaded properly based on size. Fingers crossed. That was a lot of downloading SRA Downloads

It turns out we weren’t as lucky as we thought with our PBjelly run on Hyak as we thought, we hit our expanded file # allocations somewhere before it quit, so it failed to actually write the output files to disk. No error, no email. Just no files. That’s not annoying at all. I’ve got some help desk inquiries to the Hyak people asking about how to write temp files to the execute node we’ll be using, hopefully avoiding any /gscratch/ associated file number limits.

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