Hi
I used Qiime1 before successfully, but I downloaded Qiime 2 today and I imported my FASTQ files from paired-ended Illumina platform. I would like to describe me the steps to do the analysis. The files are demultiplexed. Thanks
Bassam
Hi @babomoelak,
As a former QIIME 1 user, you may find the moving pictures tutorial familiar. You may also want to read the qiime2 for experienced users page.
In general, I think the tutorials are a pretty good reference for commands/possible analysis workflows.
In addition, you may find the plugin library useful to explore new options for analysis.
Best,
Justine
Hi Justine
Thanks for reply. The files from Illumina that I generated are in the shared folder in qiime2. They are demultiplexed into forward and reverse. Should I join them first. They are gz filed. Or should I denoise them first. Also what is the correct commands for such operations. Sorry for so many questions but it is the start for me in Qiime2.
Bassam
Hi @babomoelak,
Typically, I find it easier to import sequences because I like QIIME 2's provenance tracking. So, I would import first. The other specific questions are hard for me to answer, becuase there are multiple paths. You may want to look at the Atacama soil tutorial for paired end sequences with dada2 and the Alternative methods of read-joining tutorial for deblur.
Because there's not a one size fits all pipeline, the answer truely depends on what you want to do. My suggestion is to spend some time with the tutorials, I find them really useful for figuring out where to look for commands.
Best,
Justine
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