Question: Extract V3-V4 regions from 16s sequences
0
gravatar for Florian Plaza Oñate
3.7 years 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 • 3.7k views
ADD COMMENTlink modified 2.2 years ago by Dattatray Mongad350 • written 3.7 years ago by Florian Plaza Oñate0

Thanks. I will try it.

EDIT: It works very well. Thanks again.

ADD REPLYlink modified 3.7 years ago • written 3.7 years ago by Florian Plaza Oñate0

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

ADD REPLYlink written 3.7 years ago by Picasa540

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 3.7 years 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 2.3 years ago by Dattatray Mongad350

Could you please share your script?

ADD REPLYlink written 2.2 years ago by samedsaka0
2
gravatar for lakhujanivijay
3.7 years ago by
lakhujanivijay5.1k
India
lakhujanivijay5.1k wrote:

Check out V-Xtractor

Though, I never used.

ADD COMMENTlink written 3.7 years ago by lakhujanivijay5.1k
1
gravatar for Dattatray Mongad
2.2 years ago by
National Centre for Cell Science, Pune
Dattatray Mongad350 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 2.2 years ago • written 2.2 years ago by Dattatray Mongad350

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 2.2 years ago • written 2.2 years ago by genomax87k

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

ADD REPLYlink written 2.2 years ago by samedsaka0

Hello what are the primers you used, im getting an empty file? can you enlighten me please?

ADD REPLYlink written 8 months ago by nilaylale880

For my work, I have used modified primers for V4 (515f-806r) region of 16S rRNA gene as mentioned in Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys

-f GTGYCAGCMGCCGCGGTAA -r GGACTACNVGGGTWTCTAAT

ADD REPLYlink written 8 months ago by Dattatray Mongad350
0
gravatar for liqing1123
3.1 years ago by
liqing112310
liqing112310 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 3.1 years ago by liqing112310
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