reference genome for 16S rDNA sequences in NGS analysis

Question

[Ybanet]

Hello all,

I'm new to bioinformatics and I'm doing my research work with 16S rDNA NGS analysis.I have 16S rDNA sequenced data in fastq format. Now I stuck with picard tool 's Mark Duplicates step. In here I need a reference genome for alignment. I use NCBI 16S microbial DB for Blast step.

Can anyone help me to solve this?

[Carlo Yague]

So your reference genome is the NCBI 16S microbial sequences, no ? However, I don't really understand why you use markduplicate along with blast... Can you provide a bit more details about your workflow and what you want to achieve ?

[jazebe_1461]

Hi, if you are interested in analysing your 16S Data using Qiime2, I can cooperate with your project.

Answer 1

[Daniel]

I think you're probably jumping in wrong to this and using tools that you know the name of.

If you have a 16S rRNA dataset you probably want to use qiime/mothur, and I recomend working through this first: http://qiime.org/tutorials/tutorial.html