Eli Roberson (he/him)

#bioinformatics #genomics

Do I know anyone working with #nanostring #GeoMx? This is the first GeoMx dataset we've received.

There appear to be several packages for upfront QC and transfer to Seurat of the *processed* data in R. But I wasn't sure if there was anyone with recommendations for taking FASTQ to DCC. The instructions for installing and running the Nanostring pipeline don't seem very friendly to pure command-line interaction on a local server of in self-contained docker image.

Feb 17, 2023 at 3:35pmWeb
Show threadElisabeth LodderFeb 17, 2023
@thatdnaguy hmmm ours only just got installed so I don’t know anything yet. But I have been told that all their pipeline stuff is on GitHub. So there should be a way to do this in R only, as that’s where the pipeline gets developed. Let me know if you figure something out!
Show threadEli Roberson (he/him)Feb 17, 2023
@eml314 I've been able to find quite a bit of stuff for getting the DCC files into our doing QC and formatting tips to get it into Seurat. But most of what I'm seeing about getting the fast queue to a DCC file requires using their software. And at least based on the description of how it works it isn't overly complicated. I'd much rather get it set up so that I can just make it a snake make workflow with our standard docker images rather than having to deal with installing their service.
Show threadEli Roberson (he/him)Feb 17, 2023
@eml314 I'll let you know what I can dig up