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BigelowLab / edna-dada2

Maine eDNA dada2
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PacBio Workflow #4

Closed robinsleith closed 3 years ago

robinsleith commented 3 years ago

We will be doing more and more pacbio sequencing and it would be good to have a script and config file setup for processing those data. It is possible we could add elements to the existing config and script and have one that does both, open to suggestions! I have a MRE and maybe @btupper and I can get together and run through that.

btupper commented 3 years ago

Sure. Tell me what MRE is?

robinsleith commented 3 years ago

I guess it depends who you are talking to, either https://en.wikipedia.org/wiki/Minimal_working_example or https://en.wikipedia.org/wiki/Meal,_Ready-to-Eat

btupper commented 3 years ago

Ha! Thank you!

robinsleith commented 3 years ago

@btupper do you have time today or tomorrow before 12 to talk pacbio pipeline?

btupper commented 3 years ago

How about 11 today?

btupper commented 3 years ago

See https://github.com/BigelowLab/dadautils/commit/2afb494347ae9ad0f17e803f48f64766950fffea

list_filepairs() for pacbio will yield an empty character string for pacbio. You can set the require_reverse argument if you want to enforce it for Illumina.

run_dada() filter_and_trim() and learn_errors() are now pacbio savvy. Plus ancillary functions like plotting.

My guess is that there will be others I didn't catch. Anywho, reinstall dadautils

devtools::install("/mnt/storage/data/edna/packages/dadautils", upgrade = FALSE)

And give it a pacbio shake.

btupper commented 3 years ago

Have you tried this yet?

robinsleith commented 3 years ago

Yeah! Sorry for not updating you! Its working!