Question: reference genome for 16S rDNA sequences in NGS analysis
0
gravatar for Ybanet
2.5 years ago by
Ybanet0
Sri Lanka
Ybanet0 wrote:

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?

genome alignment 16s next-gen ref • 813 views
ADD COMMENTlink modified 2.5 years ago by Daniel3.6k • written 2.5 years ago by Ybanet0

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 ?

ADD REPLYlink written 2.5 years ago by Carlo Yague4.2k
1
gravatar for Daniel
2.5 years ago by
Daniel3.6k
Cardiff University
Daniel3.6k wrote:

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

ADD COMMENTlink written 2.5 years ago by Daniel3.6k
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