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Forum: Bioinformatics 11-06-2014, 11:13 AM
Replies: 5
Views: 1,998
Posted By James88
I ended up giving up installing it on my Linux...

I ended up giving up installing it on my Linux laptop and did a clean install of Linux on a partition of my Windows computer.

Then installed on there and it worked... Didn't really SOLVE my...
Forum: Bioinformatics 11-06-2014, 11:10 AM
Replies: 1
Views: 1,176
Posted By James88
I sorted this by pestering a bioinformatician I...

I sorted this by pestering a bioinformatician I know that uses orthAgogue.

I basically entered the command incorrectly.

Where this produced an error:

orthAgogue all-vs-all_test -t 1 -p 2
...
Forum: Bioinformatics 11-05-2014, 02:50 AM
Replies: 1
Views: 1,176
Posted By James88
OrthAgogue Buffer Overflow Error

Hello folks,

I'm trying to use a piece of software called OrthAgogue (https://code.google.com/p/orthagogue/wiki/manual).

It's supposed to be similar to OrthoMCL but without the unpleasant SQL...
Forum: Bioinformatics 11-05-2014, 02:45 AM
Replies: 4
Views: 1,862
Posted By James88
I had already... acquired one from the Kostas lab...

I had already... acquired one from the Kostas lab but have since been told that I apparently don't need it as we're using OrthAgogue now which allegedly does the reciprocal blast from an input of an...
Forum: Bioinformatics 11-05-2014, 02:41 AM
Replies: 5
Views: 1,998
Posted By James88
Thank you for the help. It was all the...

Thank you for the help. It was all the encouragement I needed to carry on and get PROKKA working and ditch Glimmer!
Forum: Bioinformatics 10-29-2014, 08:43 AM
Replies: 4
Views: 1,862
Posted By James88
Thank you for the reply/advice. I agree... That...

Thank you for the reply/advice. I agree... That certainly felt like the most sensible thing to do. I had better get writing a little script!
Forum: Bioinformatics 10-29-2014, 08:38 AM
Replies: 5
Views: 1,998
Posted By James88
Glimmer vs Prokka

Hello,

I am wondering if there is some cross-over in the functions of Glimmer and Prokka. As I understand it, Glimmer is able to predict orf's and extract them. Prokka is is used for annotation....
Forum: Bioinformatics 10-28-2014, 12:48 PM
Replies: 4
Views: 1,862
Posted By James88
Reciprocal Blast Guidance...

Hello,

I'm working on creating a core set of orthologous genes in ~40 c.diff strains in order to create a binary tree at the end.

I was told to use reciprocal blast searches. I understand this...
Showing results 1 to 8 of 8

 


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