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I am getting the error "cannot read line XX, line is too long" when opening a fasta file with readDNAStringSet. It seems to be because the headers of some sequences are very long. Would it be possible…
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Hi,
I work on two datasets generated separately : Metagenome assembled genomes for virus, and 16S for bacteria.
I would like to know if spieceasi can be applied to this kind of analyses with combine…
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The "otu_class_appr" and "otu_db" fields both seem useful for metabarcoding data (unless denoising/ASV generation was applied). However their descriptions are tailored to (viral)genomes. I suggest we …
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I believe `scripts` has been replaced by `bin`, and so paths pointing at `scripts` are broken.
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I'm working with metabarcoding of fungi associated with plant tissues. After processing the data through the DADA2 ITS Pipeline Workflow (1.8) I realized through the taxonomy table that there is a lar…
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- submit sequences to NCBI
- submit occurrences to OBIS
Get insight from Diana's presentation.
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Hi,
I came a cross a weird by chance while going through my BOLDigger output file.
I have ~8,000 COI metabarcoding sequences which I classified with BOLDigger. I was using boldigger-cline v2.1.…
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`fastq_location` argument passed from the wrapper script maybe should not have a trailing slash, because it creates a double slash in various paths and wrecks things.
Same thing happens with `outpu…
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- Paper: https://www.authorea.com/users/330161/articles/457029-fishcard-fish-12s-california-current-specific-reference-database-for-enhanced-metabarcoding-efforts
- GitHub: https://github.com/zjgold/…
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`bash metabarcoding_wrapper.sh {pathway to muri_metabarcoding} {run name}` requires a specific format of run name, I believe, but I don't know what it is. Also, should that run name be given as a quo…