RobertsLab
Download Pacific cod data to Roberts Lab Server
Azenta WGS is complete for the Pacific cod marine heatwave genetics project and pilot ecotype project. I'm downloading to NOAA server now. I can also download it to a Roberts server via ftp (if so which one?), or provide the login info.
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 data inventory spreadsheet, but here is the high-level:
- All cod, WGS (moderate coverage)
- 30-1149633765: heatwave genetics study of juvenile cod spanning 2008 - 2023 + six experimental fish that needed resequencing for juvenile temperature study.
- 30-1149634506: pilot cod ecotype sequencing (shallow, deep)
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 % overrepresented sequences (most from one year - 2013). The samples from 2008 look okay! I'm trimming things now, will report back.
Raw data multiqc: https://github.com/laurahspencer/heatwave-genetics/blob/main/data/multiqc_report_raw.html
Here's Azenta's report: https://github.com/laurahspencer/heatwave-genetics/blob/main/data/Azenta_30-1149633765_Data_Report.html
Unfortunately, using the GitHub HTML preview thingy doesn't really work well for MultiQC reports. Can you post link to HTML file from one of the birds (e.g. Owl or Gannet)?
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