Hello Members, and Seniors,
I don't have any experience in/on 16s RNA data.
I know there are tools like QIIME, and mothur which do the taxonomic assignments, and are too versatile in themselves bundled with many more utilities. I've both these tools installed and working fine.
I'm looking for few guidelines, or steps in order to move ahead.
I've Illumina data.
Is there something similar to assembly?, such as :-
In amplicon data, they are barcoded, and then demultiplexed, uh; this is making the water more muddy for me
Can somebody please enlighten here with initial steps/workflow?
The first few steps are trimming, denoising, and chimera removal, if I'm not wrong.
And how do these tools (QIIME, Mothur) come into picture and where?
I don't have any experience in/on 16s RNA data.
I know there are tools like QIIME, and mothur which do the taxonomic assignments, and are too versatile in themselves bundled with many more utilities. I've both these tools installed and working fine.
I'm looking for few guidelines, or steps in order to move ahead.
I've Illumina data.
Is there something similar to assembly?, such as :-
- get fastq (either paired end (either mate paired, or normal), or single-end),
- trim your reads (with tools like timmomatic, etc)
- assemble your reads (based on your type of organism, if prokaryote-SPAdes, if not find the suitable one)
- Get QUAST report, and check/verify results.
- trim your reads (with tools like timmomatic, etc)
- assemble your reads (based on your type of organism, if prokaryote-SPAdes, if not find the suitable one)
- Get QUAST report, and check/verify results.
Can somebody please enlighten here with initial steps/workflow?
The first few steps are trimming, denoising, and chimera removal, if I'm not wrong.
And how do these tools (QIIME, Mothur) come into picture and where?
Comment