C. Titus Brown

Still working on this.

running diffexp on examples/nema.yaml doesn't do anything?

3

I first ran: ``` ./run_eelpond examples/nema.yaml ``` which completed successfully, and then ran: ``` ./run_eelpond examples/nema.yaml diffexp ``` which did... nothing? The output did include ``` deseq2: /mnt/research/ged/ctb/eelpond/nema_out/diffexp for explanation...

how should we generate the gene to transcript map?

6

@ljcohen has some code, maybe... :)

document and test --extra_config

2

feature added in #37, see #25 for root issue.

make 'salmon' or 'quantify' an equal citizen

1

A common use case for transcriptomics doesn't involve de novo assembly, but rather just quantification or (perhaps) annotation + quantification, for semi-model organisms like dog and cat which have good...

is busco completeness output available anywhere?

2

I know busco is run as part of dammit but it doesn't seem like busco completeness evaluation is available anywhere.

if I remove the `assembly/` output directory, shouldn't eelpond rerun everything after that too?

2

right now if you remove the assembly directory, and then run `default`, eelpond shrugs and does nothing because all of its targets are available. this seems wrong overall.

dammit step fails after rerunning assembly

1

if I remove the assembly, and then `run_eelpond trinity default`, the dammit step fails. output below. I can get it to work properly by removing the annotation directory. I suspect...

'basename' may not be properly quoted

2

a student used a space in 'basename' in the config yaml file, and it looks like that will break shell commands that aren't properly quoted. I *think* single quotes should...

https://www.biorxiv.org/content/10.1101/326363v4?rss=1