Question: Extract V3-V4 regions from 16s sequences
0
gravatar for Florian Plaza Oñate
22 months ago by
France, Paris area
Florian Plaza Oñate0 wrote:

Hi, I have a set of full-length 16s genes in a multi FASTA files. I am looking for a tool to extract all the v3-v4 variable regions. Thanks in advance.

16s analysis • 1.7k views
ADD COMMENTlink modified 5 months ago by doctor.dee005170 • written 22 months ago by Florian Plaza Oñate0

Thanks. I will try it.

EDIT: It works very well. Thanks again.

ADD REPLYlink modified 22 months ago • written 22 months ago by Florian Plaza Oñate0

Just a question, how did you sequence full 16s genes ?

ADD REPLYlink written 22 months ago by Picasa380

I have downloaded them from SILVA. I should change the question tags. However, I know that some labs get full length 16s with PacBio sequencers.

ADD REPLYlink written 22 months ago by Florian Plaza Oñate0

I had downloaded greengenes, SILVA and RDP full length 16S rRNA gene databases and used universal primers of V4 regions to scan against each sequence by fuzznuc (emboss toolkit). If required I can share my python script.

ADD REPLYlink written 5 months ago by doctor.dee005170

Could you please share your script?

ADD REPLYlink written 5 months ago by samedsaka0
2
gravatar for Vijay Lakhujani
22 months ago by
Vijay Lakhujani3.1k
India
Vijay Lakhujani3.1k wrote:

Check out V-Xtractor

Though, I never used.

ADD COMMENTlink written 22 months ago by Vijay Lakhujani3.1k
1
gravatar for doctor.dee005
5 months ago by
doctor.dee005170
Bioinformatics Center, Pune
doctor.dee005170 wrote:

You can find the script here. Just install emboss toolkit or make sure you have fuzznuc in your path. Let me know your experience, I will improve it if needed. This script uses given primer sets (reverse and forward) to extract the region which can be amplified. So you can use the primers accordingly. For example, here u can use forward primer fo V3 region and reverse primer for V4.

Usage:- python3.6 extract_n_multiplex.py [options] Options: -h, --help show this help message and exit -f FORWARD_PRIMER forward-primer -r REVERSE_PRIMER reverse-primer -n NITER (default 1) number of iterations to repeat random multiplexing of extracted sequences -d SEQDATA multifasta sequence file from which regions will be extracted.

ADD COMMENTlink modified 5 months ago • written 5 months ago by doctor.dee005170

Please add a bit more information to your post by editing it. What script are you referring to? What does it do? It would be useful to add that information in your post. is this script meant to be used to solve the original question posted in this thread?

ADD REPLYlink modified 5 months ago • written 5 months ago by genomax57k

I used your script. It works well. Thank you.

ADD REPLYlink written 5 months ago by samedsaka0
0
gravatar for liqing1123
15 months ago by
liqing11230
liqing11230 wrote:

Dear all, I have got the same problem. I would like to extract all the v3-v4 region from silva.bacteria.fastq file. After consulting to the MISEQ SOP for mothur, I have used the command line as below. But I'm not sure about the start and end position for V3-V4 region. Can someone help to share their experience? Great appreciate for your help.

mothur "#pcr.seqs(fasta=silva.bacteria.fasta, start=6388, end=25319, keepdots=F,processors=8)"

Lola

ADD COMMENTlink written 15 months ago by liqing11230
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