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I know that some people have/are using Taxonium for bacterial genomes. I suspect that this probably poses some issues with e.g. the number of mutations on each branch which might get overwhelming. If …
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Good Afternoon.
Orthofinder team.
I have run the Orthofinder (./orthofinder -f mydata) process with 1000 proteomes of different bacteria species, After some days, I had some erros in order to gene…
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Hi , I had configured the NCBI STAT tool as per the steps mentioned in https://www.ncbi.nlm.nih.gov/sra/docs/sra-taxonomy-analysis-tool/ and was able to successfully run the input file given in Examp…
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I tried to to re-run WITCH after termination due to unexpected server down, but WITCH fails to retrieve file.
In fact, there is no directory named /data/genome/run/snyoo/programs/WITCH/results/Bacter…
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Hi,
I have two libraries that I am having problems with the bacteria_tradis mapping for. I have used cutadapt to trim the transposon (and adapters) from the reads and selected only the reads that c…
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To obtain the krona visualization of Bracken reports, I run the kreport2krona.py using the file bracken_kreport (percentage of reads, Total number of reads, etc). However, I noted that the created ou…
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Firstly, I am in AWE of your work, and I hope to marry it with https://skewdb.org/ at my earliest convenience. This is database of GC skews of bacterial and archaeal chromosomes.
I downloaded http…
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New term request Bacteria in peritoneal fluid (nadea3_200115185424): UMLS: 5154140
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I notice that the top-ranked bacteria are sometimes caused by outliers of `linda` analysis. This happens when some samples have five species and other species have fifty species detected, for instance…
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Hi,
I have been running MDMcleaner on 2 different bin sets. In one run, not all bins were processed without error (see #37). Using the same reference data, I am now getting the following error for…