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Hi,
I'm trying to simulate reads for individual genes. However I noticed that after aligning, the read depth in the first few hundred and the last few hundred bases of each reference sequence is lowe…
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When using sff_extract (seq_crumbs 0.1.8) on SFF files that contain amplicon reads, I get the warning:
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WARNING: weird sequences in file /srv/whitlam/bio/data/pyrotags/raw/Gasket67/Gasket67.sff…
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Raising this issue to be followed up once we have a release candidate to evaluate.
Theo Sanderson spotted that if we look at spike 142, and colour a tree by genotype at that position, it looks a b…
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I initially discovered this while building the 2024.5 docs, but also replicated locally. Within a 2024.5 amplicon environment (on mac OS) the command in PD mice that utilizes ancombc with `donor * gen…
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Hi, Dr. Hu. I met error when I performed differential analysis by LOCOM. The following is my codes:
The amplicon_ps_genus.RDS dataset is [here](https://github.com/XbiomeAnalysis/Microbiota_notes/…
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Dear Jennifer,
while installing q2-ghost-tree to the qiime2 version 2022.8, I got the error message
NameError: Duplicate view registration ('AlignedRNAFASTAFormat') defined in plugins: 'ghost-tree' …
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The accession BK010471 is for a crAssphage that is ubiquitous in human gut metagenomes ([link](https://www.nature.com/articles/ncomms5498)), and in particular is found in the 454 data set SRR073439.
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We are planning to benchmark a set of metabarcoding tools and I thought to use OPAL. When investigating the tool, I thought one could use it for metabarcoding assessment just as well as long as one ca…
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Good afternoon!
These two tools seem similar in some ways, and I would appreciate your feedback how how they differ in approach and intended usage.
>a rare read is erroneous if it has a neighbor…