Confluence Retirement

Due to the feedback from stakeholders and our commitment to not adversely impact USGS science activities that Confluence supports, we are extending the migration deadline to January 2023.

In an effort to consolidate USGS hosted Wikis, myUSGS’ Confluence service is targeted for retirement. The official USGS Wiki and collaboration space is now SharePoint. Please migrate existing spaces and content to the SharePoint platform and remove it from Confluence at your earliest convenience. If you need any additional information or have any concerns about this change, please contact Thank you for your prompt attention to this matter.
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Description: (from Scott Cornman,

For this month's call, I'll lead a roundtable and try to answer questions you may have regarding RNA-seq (measuring gene expression with high-throughput sequencing). Pretty informal, for those with a basic understanding already of what RNA-seq involves. The goal is to share best-practice tips, get people past any specific roadblock, and seek consistency in the data release process (should anything extra be released if the raw data is in GenBank and the workflow is described in a manuscript?)

I'll create a forum page with my basic workflow and some possible discussion points. I'll also have a few example slides but not with the intention of lecturing at folks. Feel free to bring your own data issues, we can share the webex control quite easily. We can repeat this or a similar forum again as interest dictates, and it need not be during the regular scheduled slot.


RNA-Seq workflow elements Forum page


Please comment on the Forum page with any alternate suggestions or other notes. (Email if you need help accessing the comment feature of the forum - most Bioinformatics WG members should have the correct permissions.)


Some highlights:

  1. Scott reviewed some common data exploration visualizations
  2. For USGS Data Release, one suggested path is to share the counts table - anyone can take the counts table to reproduce results or do the same exploration, but it is very computationally expensive to produce the counts table.
  3. For people interested in learning R, a general R course could be very useful because of the learning curve - you don't necessarily need a sequence-data focused R course.


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