Laura H Spencer

I cannot reproduce the figures in the [gene expression](https://grunwaldlab.github.io/metacoder_documentation/publication--09--gene_expression.html) example. I successfully generate the final list of significant genes with their GO terms (final `res` object) ``` > head(res) log2...

I'm also interested in running this pipeline with single end reads

We have the exact same issue! @alexyfyf did you identify a cause of your empty output files? Better yet, a solution?

I downloaded via sftp to NOAA server, checked hashes (md5sum), then rsynced from NOAA server to nightengales: /volume1/web/nightingales/G_macrocephalus/ 30-1149633765 and 30-1149634506 I am in the process of updating the nightengales...

Started assessing this data - raw data multiqc report below for the big batch of samples, the Pacific cod heatwave genetics project. About 25 samples look bad - very high...

Here's the [multqc report after trimming](https://htmlpreview.github.io/?https://github.com/laurahspencer/heatwave-genetics/blob/main/data/multiqc_report_trimmed.html)

HTML files can be downloaded here: - Raw: https://github.com/laurahspencer/heatwave-genetics/blob/main/data/multiqc_report_raw.html - Trimmed: https://github.com/laurahspencer/heatwave-genetics/blob/main/data/multiqc_report_trimmed.html Happy to upload to Owl if you'd like them there too

Yes!

Cod blood samples for this test DNA + RNA extraction. I've provided 8 (4 each for treatment, 5C and 9C) in case any of these samples are missing or have...

I'd like to move forward with extracting RNA & DNA from all blood samples (four temperature treatments, 0C, 5C, 9C, and 16C). Max number of samples per temperature is n=40....