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In your repo, generate a Jupyter notebook where you begin to explore your data.
Be sure to show aspects including, size, number of reads, format, and any metadata.
This should be some form of sequen…
sr320 updated
3 years ago
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last § of section 1.4: Maybe to tone down or reformulate a bit. There are actually numerous studies for which data are not stored in these repositories because these were built so that to host metabar…
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Comments and suggestions from @birgitgemeinholzer about figure 2:
- instead of "denoising" perhaps "quality filtering"?
- in the legend: "here exemplified by metabarcoding" metabarcoding versus eD…
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There underlining looks bad in some sections for some reason...
https://docs.gbif-uat.org/publishing-sequence-derived-data/1.0/en/#mapping-metabarcoding-edna-and-barcoding-data
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This is focused on metabarcoding studies, but metagenomics is also briefly mentioned. I guess adding information from metagenomics datasets is another challenge, maybe there could be some mention of p…
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Comment from AW about the following sentence:
> This is the case for **most metagenomics, metabarcoding** and eDNA studies.
Comment:
> I am not sure if this holds really true for MOST metabarcodi…
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How could you use alignment data (and samtools) in your own project?
Provide a least one example of what said code might look like.
sr320 updated
3 years ago
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1.3. Introduction to sequence-derived occurrence data describes eDNA in much detail, but i think it would also be appropriate here to intoduce/define the terms "DNA barcoding" and "metabarcoding", sin…
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In the description fields of basisOfRecord, the links to the different categories is not up to date and need to match the revision. E.g. in Table 4: Recommended fields for Occurrence core for ddPCR/qP…
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Hi @benjjneb,
I am having issues with dada2's assignTaxonomy output. Performing the dada2 workflow as usual for metabarcoding analysis, I have inferred ~8000 ASVs from COI amplicon sequence reads (…