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reference genome for 16S rDNA sequences in NGS analysis

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?

next-gen alignment ref genome 16s
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updated by jazebe_1461 • jazebe_1461 • written by Ybanet • Ybanet

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 ?

• 1 views • link
written by Carlo Yague Carlo Yague

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

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written by jazebe_1461 • jazebe_1461

1 answer

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

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written by Daniel Daniel

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