diBayes

[jonasZ]

Hello everybody,

i am trying to use the Solid diBayes tool for SNP detection (http://solidsoftwaretools.com/gf/project/dibayes/). In the documentations it is said, that i need to create the position error file and the probe error file by using corona v3 jmoap_module.sh.
The only corona i found is this one (http://solidsoftwaretools.com/gf/project/corona/) and this does not contain the jmoap-script.

does anybody know how i get the position error file and the probe error file without this script (or where i can get this script)

thx
Jonas

[westerman]

Good question. I suspect that most of us now use Bioscope instead of Corona however, as far as I know, the former is still restricted from general use.

My copies of both Corona and Bioscope do not contain the jmoap-script so I am not sure what the dibayes documentation is referring to. If you send email to Lifetech/SOLiD support then they might be able to help (although Corona is unsupported) or, better yet, give you access to Bioscope (which includes a newer version of diBayes).

[jonasZ]

hi,

thx for your answer.
As far as i know bioscope is not free available, but i think i will write a mail to their support to ask them about these script.

thx again, bye

[Fabian]

Even when you had to generate those position error files, it was not exactly straight forward. As mentioned, Bioscope is your best bet. They simplified all of those pipelines via this package. If you have an instrument, it should be free(?), otherwise I'm not sure the cost.

[SOLiDance]

Fabian is rt, Bioscope is quite easy to learn&use. It's free with the SOLiD instrument,and only can be installed on computer clusters,not a laptop or desktop(Just heared, didn't try it~)

[Fabian]

Fabian is rt, Bioscope is quite easy to learn&use. It's free with the SOLiD instrument,and only can be installed on computer clusters,not a laptop or desktop(Just heared, didn't try it~)

This is also correct. I have it installed on our dedicated cluster (not on the instrument cluster) and it's worked well. You can also install in on a communal cluster as a user, but I believe that only gives you CLI functionality, not the GUI capabilities.

If you can get it running, I would recommend diBayes use for SOLiD data. We've done some work in validation and the p-Value with their statistical model has some decent predictive capability. That is to say variants with low p-Values correlated with a higher ability to validate in the lab.

[Zaag]

I runned the tool but I only get variants in IUB code, but I would like a consensus nucleotide (only ACTG).

Is this possible with diBayes or is there a way to convert this?

[Fabian]

I runned the tool but I only get variants in IUB code, but I would like a consensus nucleotide (only ACTG).

Is this possible with diBayes or is there a way to convert this?

To my knowledge, diBayes will not convert these. I've written in house scripts that take the output of diBayes and annotate further. See attached. To my knowledge, most annotations are done by in house scripting or you could try something like annovar.