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Hi, I am running CAT to annotate contigs from metagenomes that are known to be E. coli by several other approaches. For example, greater than 99% average nucleotide identity with reference E. coli ge…
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First, all reads are merged.
We skip the CO_ and CH_ as they contain all reads for hostplant respectively.
```
ls -1 05-CLEAN-MERGED/* | paste - - | grep -v "CO_" | grep -v "CH_" > doc/all-clean-re…
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I’m getting the following error with SIDEARM:
```
(sidearm) bash-4.2$ cwl-runner --preserve-environment BLASTDB --preserve-environment PERL5LIB /Software/sidearm/bin/cwl-runner 1.0.20170413194156
R…
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I ran krakenuniq-download as follows:
krakenuniq-download --db krakenU --threads 128 --dust refseq/bacteria
$ krakenuniq-download --db krakenU --threads 128 --dust refseq/bacteria
Downloading assem…
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Dear developers,I hope this message finds you well.I ran Eggnog Mapper with the parameters "-tax scope bacteria" and without the "-tax scope bacteria" parameter on my bacterial genomes. I noticed …
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wget http://files.cgrb.oregonstate.edu/Koslicki_Lab/MetaPalette/Bacteria.tar.gz fails for me. It says access forbidden. I would appreciate your guidance.
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### Enter your question -
You have a Petri dish with bacteria and you are preparing to dive into the harsh micro-world. But, unfortunately, you don't have any microscope nearby, so you can't watch t…
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- Second sentence in `Definition` looks like it could benefit form some clarification. Do we mean to say that the user should be careful to include phenotypes covering all of the different intermediat…
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I have metagenmoic data, i would like to analyse the bacteria and yeast (separately) removing kindgom e.g. viruses etc is there a way to filter these out?