Question: looking for 16S RNA sequence consensus
0
gravatar for sacha
2.1 years ago by
sacha1.5k
France
sacha1.5k wrote:

I m looking for a 16s RNA sequence consensus ? Does it exist ? I want to make some alignement, to know exactly where my read comes from . Does my read comes from V3 or V4 region more precisely.

sequence rna16s • 1.4k views
ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by sacha1.5k

What about the fasta sequence ?

ADD REPLYlink written 2.1 years ago by sacha1.5k

Please use ADD COMMENT/ADD REPLY when responding to existing posts/comments. SUBMIT ANSWERS is only for NEW answers to original question.

ADD REPLYlink written 2.1 years ago by genomax55k

What fasta sequence do you want?

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by genomax55k

I m looking for a 16S RNA fasta sequence. My objectif is to align a fastq on this reference using bwa.

ADD REPLYlink written 2.1 years ago by sacha1.5k

Are you interested in a specific bacterium? As linked below SILVA database has this file (or use one of the other db) which will have many organisms so you can select the sequence that you want from that file.

If you are looking to classify a metagenomic dataset then Kraken or Kaiju would be better options.

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by genomax55k
2
gravatar for shenwei356
2.1 years ago by
shenwei3564.1k
China
shenwei3564.1k wrote:
ADD COMMENTlink written 2.1 years ago by shenwei3564.1k
0
gravatar for sacha
2.1 years ago by
sacha1.5k
France
sacha1.5k wrote:

Same question there Where Do I Find The 16S Rdna Reference Sequences (Metagenomics)

ADD COMMENTlink written 2.1 years ago by sacha1.5k
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