Operon prediction in RNA-Seq - How?
1
0
Entering edit mode
6.0 years ago
R.Blues ▴ 160

Hello everyone,

I would like to ask if there is a standardized procedure to predict operons in bacteria from RNA-Seq data, preferably in R. I would compare two conditions with three replicates each.

Currently I am thinking of using the CONDOP package (https://cran.r-project.org/web/packages/CONDOP/CONDOP.pdf), but I would like to hear your opinions. Maybe there is an optimum strategy for this that I haven't seen.

What do you think? What would you recommend?

Thank you very much.

operon RNA-Seq R CONDOP • 1.6k views
ADD COMMENT
1
Entering edit mode
6.0 years ago
Asaf 8.7k

I think that you should build a transcriptome from each library and compare them. If this is your major goal, you can use sequencing methods that will sequence the 5' and 3' ends of RNAs to get better resolution like in here: http://www.ncbi.nlm.nih.gov/pubmed/27120414

ADD COMMENT
0
Entering edit mode

Hmm.. yes, that is another possibility, but... wouldn't building this transcriptome create noise and false transcripts? What would you use to build it, Trinity?

Thank you very much, Asaf.

ADD REPLY
0
Entering edit mode

I don't think it will add noise, unless the expression of the operon/gene is low. Since you have the reference genome you can use something like cufflinks

ADD REPLY

Login before adding your answer.

Traffic: 1312 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6