wfgui

> Hi, I will debug within some days. I had the same problem， can't remove read2 adapters

> Right, filtering is recommended. The current default cutoff (0.5) is set based on simulated virome data from known genomes. With real metaG data that have more unknown sequences, the...

> @hjdong, Do you mean these two sequences are both in `final-viral-combined.fa`, but you can not find the second one in `final-viral-score.tsv`? If so, could you paste the sequence of...

> original sequence Here is the original sequence for VirSorter2(version 2.0.beta).Contigs less than 1 kb in length were discarded. My command: ``` virsorter run -w SRR9161490 -i SRR9161490.contigs.1k.fa.txt -j 12...

> For pulsar, X can be any data matrix. Does spiec easi perform clr transformations on data matrices before running？ If I input a CLR data matrix, will the steps...

> Yes > […](#) > On Wed, Aug 7, 2024, 5:25 AM wfgui ***@***.***> wrote: For pulsar, X can be any data matrix. Does spiec easi perform clr transformations on...

I also had a seemingly simple question about whether I could format the output at taxonomy, such as converting it to k__; p__; c__; o__; f__; g__; s__. Thanks!

 What's the difference between "Unclassified" and "Viruses;;;;;;" ?

> Hi, The probable cause of the issue is in the data normalization. The "-o 1000000" in "python format_input.py" command means that the maximum value after normalization will not exceed...

> Median. Same with the lefse python version. I ran the code the way you recommended. I found at the species level that the direction of enrichment is very different...