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Hi Jody,
Which reference genomes do you recommend using for M. abscessus? I understand that each of the three subspecies:
M. abscessus subspecies abscessus, M. abscessus subspecies ma…
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I am working with a plant dataset that seems considerably larger than other projects I see on bioinformatics forums.
In short, I have 100 paired-end, 150 cycle RNA-seq libraries with roughly 40m read…
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Hi David,
I've managed to run OGT prediction on my own metagenome assembled genomes (MAGs), using the models present in the data/prediction_demo/regression_models/ directory.
The results seem to m…
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Dear authors,
I am attempting to run the entire [viral identification SOP](https://www.protocols.io/view/viral-sequence-identification-sop-with-virsorter2-bwm5pc86?step=1) on the test dataset.
I…
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Implement rRNA prediction on contigs
cc @jgolob
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Dear developers,
For my analysis, I'm trying to disentangle what happens to the rRNAs (and tRNAs) that have been identified in the first steps. I see that in the intermediate folder, there is a mas…
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I found the abundance ASV performed difference significant when you normalized by marker gene copies(After this step, ASVs show a difference in each sample.). Likewise, it would perform a big differe…
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Hello,
I went through the whole pipeline of funannotate and was able to obtain the Json file. The file output is :
{
"assembly": {
"num_contigs": 9557,
"length": 994064042…
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I found a patent sequence (FV537213.1) in cov2.fa which is obviously non-biological (no Cs!) and causes problems for sequence search and comparison algorithms because it is low complexity. Perhaps we …
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Hi,
Thanks you guys in advance!
I met a couple of questions of the PICRUSt2 (hopefully not stupid), could you please give me some clue if you're free?
(1) When preforming PICRUSt2 in Qiime2, …