Question: looking for 16S RNA sequence consensus
0
gravatar for sacha
14 months ago by
sacha820
France
sacha820 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 • 741 views
ADD COMMENTlink modified 14 months ago • written 14 months ago by sacha820

What about the fasta sequence ?

ADD REPLYlink written 14 months ago by sacha820

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 14 months ago by genomax34k

What fasta sequence do you want?

ADD REPLYlink modified 14 months ago • written 14 months ago by genomax34k

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

ADD REPLYlink written 14 months ago by sacha820

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 14 months ago • written 14 months ago by genomax34k
2
gravatar for shenwei356
14 months ago by
shenwei3563.4k
China
shenwei3563.4k wrote:
ADD COMMENTlink written 14 months ago by shenwei3563.4k
0
gravatar for sacha
14 months ago by
sacha820
France
sacha820 wrote:

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

ADD COMMENTlink written 14 months ago by sacha820
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