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Based on https://github.com/iobis/Project-team-Genetic-Data/issues/8.
We currently do not have any recommendations as to how to treat controls in the publication process. It should be possible to r…
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Hi there,
I’m double checking/proofreading a DADA2 workflow script that was initially run in January of 2022 to make sure everything is still working fine.
I am running the script on the same Ill…
vmsur updated
1 month ago
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This notebook is a good start https://ioos.github.io/ioos_code_lab/content/code_gallery/data_access_notebooks/2022-11-23_pyobis_example.html
I think citations will come from GBIF, unless OBIS bring…
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We are trying to import a DWC archive from the eDNA tool into [ipt.gbif.org](http://ipt.gbif.org/).
We get these error messages:
Skipped mapped term https://w3id.org/mixs/0000050, which is unknown t…
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It should be possible to speed up the *in silico* hybridisation step by using `bwa` or similar to map candidate primers. The output of this step could be made to resemble `PrimerSearch` output to mini…
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Hi,
KTU:klustering is using a tremendous amount of memory in my machine. Even dedicating around 30 GB of swap memory and 8Gb of RAM would not be enough for around 30k input sequences (20Mb of a plain…
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Hello!
I am working on a COI metabarcoding project for animals. I currently have two database files, one fasta file containing all sequences and the other txt file containing taxonomic information …
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Dear Ben,
I have been processing metabarcoding data of the V4- 18S rDNA region (96 environmental seawater samples from a time-series).
I found that chimeras represented the 70% of total ASVs (#33…
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Hello,
I have a V3-V4 16s DNAr metabarcoding dataset of 68 samples with a read depth of 400-900K reads/sample. Samples were sequenced on a NovaSeq 6000 PE250. Primers were removed with Cutadapt, seq…
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I am interesting in post-DADA2 clustering of ASVs for more general animal biodiversity questions at the species or genus-level using, in this case, the CO1 marker. While the ASVs are very interesting …