The results that need to come out as bacteria from the barchart analyzed as Archaea according to the command tool .
In addition, when the samples that came out well as bacteria are turned along with the samples that came out as Archaea, it also comes out as Archaea.
I asked the company I sequenced and found that the sample was made up of bacteria without any Archaea.
I can't find the cause.
I analyzed using dada2 and used silva-138-99-nb-classifier.qza.
Thank you.
It is a result that came out bacteria. (fig.1)
It is a result that came out Archaea including (fig.1) results.
I am rebuilding Silva data through the link you sent me.
But it has a problem.
In Import SILVA files into QIIME 2 step, An error " 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte " appears.
I referred to the forum, but found no solution.
How should I do it?
Hi @Carlita, can you provide the exact command you are running when you encounter this error?
It sounds like you are running the semi-manual approach of importing SILVA data. You can skip all of that and simply run the commands starting with the qiime rescript get-silva-data ... step. This command wraps most of the commands under "The gritty details" section. The commands provided under that section are provided in case there is a version of SILVA that we do not provide automated access too via the get-silva-data action, i.e. where you can specify the recent versions of SILVA.
I was able to successfully run this command without any issues, and I was unable to replicate the error.
What version of QIIME 2 are you running? The latest version of RESCRIPt will run with the latest version of QIIME 2. You can install older versions of RESCRIPt, for the specific version of QIIME 2 you are running. These are available on the RESCRIPt GitHub page.
