Where do I start?! Bacterial rRNA sequencing

fmoejes · 10-01-2014, 01:23 AM

Good morning!!!

I am fairly new to the world of sequencing and bioinformatics! But as part of my PhD I am sequencing 16S rRNA to identify what bacterial consortia are present in some microalgal cultures I have!

The idea is to do Ion Torrent type sequencing of the V6 region to start identifying the bacterial consortia present.

From what I understand, we will then receive the raw data as FASTQ ( millions of reads (??)) which we then need to sort through using software such as TopHat then use rRNA databases such as SILVA to place the bacteria in a phylogenetic tree.

Do any of you have any advice of what software to use and what databases? What parameters must be set for ambiguity so my results are of a publishable quality (cross fingers)?

Any help to try and understand the bioinformatics side of things will be greatly appreciated!!

Have a lovely day all!!

GenoMax · 10-01-2014, 04:18 AM

You would not be using TopHat for the analysis you describe since it is meant for analysis of expression data.

You are interested in microbial communities, so Qiime and Mothur will likely be what you will end up using. There are tutorials availalable for Qiime (http://qiime.org/tutorials/) and Mothur (http://www.mothur.org/wiki/Main_Page).

fmoejes · 10-01-2014, 07:07 AM

Thank you so much for pointing me in the right direction, GenoMax!

Have a lovely day!

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10-01-2014, 01:23 AM	#1
fmoejes Junior Member Location: Bantry/Dusseldorf Join Date: Sep 2014 Posts: 7	Where do I start?! Bacterial rRNA sequencing Good morning!!! I am fairly new to the world of sequencing and bioinformatics! But as part of my PhD I am sequencing 16S rRNA to identify what bacterial consortia are present in some microalgal cultures I have! The idea is to do Ion Torrent type sequencing of the V6 region to start identifying the bacterial consortia present. From what I understand, we will then receive the raw data as FASTQ ( millions of reads (??)) which we then need to sort through using software such as TopHat then use rRNA databases such as SILVA to place the bacteria in a phylogenetic tree. Do any of you have any advice of what software to use and what databases? What parameters must be set for ambiguity so my results are of a publishable quality (cross fingers)? Any help to try and understand the bioinformatics side of things will be greatly appreciated!! Have a lovely day all!!

10-01-2014, 04:18 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,087	You would not be using TopHat for the analysis you describe since it is meant for analysis of expression data. You are interested in microbial communities, so Qiime and Mothur will likely be what you will end up using. There are tutorials availalable for Qiime (http://qiime.org/tutorials/) and Mothur (http://www.mothur.org/wiki/Main_Page).

10-01-2014, 07:07 AM	#3
fmoejes Junior Member Location: Bantry/Dusseldorf Join Date: Sep 2014 Posts: 7	Thank you so much for pointing me in the right direction, GenoMax! Have a lovely day!