ESapenaVentura
commented
6 months ago Reviewed the spreadsheet and the values, and overall it looks fine!
No "substantial" changes needed - In order to accelerate their submission, I am going to upload the metadata to BSD and send them back a spreadsheet with the accessions. However, over the review, there are a couple of questions we need to tackle:
- They have a lot of QC information about the reads (%GC, %Q20, etc). Need to investigate if we store that information in BSD or if we should store it in ENA (I think ENA generates this info automatically when processing reads - not sure how important it is for us to keep it. For @Jeena-Rajan and myself to discuss)
- These are not cryopreserved samples, so all the cryopreservation fields can't be filled. For now, we have filled it with the keyword "not provided", but this needs to be ammended.
- Timepoints are in a similar fashion - need to be corrected. But, since these seem to not be cryopreserved - What is the timepoint?
- Forgot to send them the "elevation" and "depth" fields with the spreadsheet, so I am going to ask her if she could fill it out
In summary, we should probably investigate these samples further, and if we can't find more info about them, set-up a short meeting with Pamela to clarify questions.
As an addendum, these are the things I changed in the spreadsheet:
- Moved site to “geographic location (region and locality)
- Used “sample_id” as “name”
- Deleted column “target” (Not filled)
- Deleted column “LUI_2023” (Not filled)
Description of the issue
To help HMGU complete their submission of reads/metagenomes and start the process to send the data through the MGnify pipelines, I would like to help HMGU submit their samples to BioSamples.
Action items