[protocols] Eel-pond/annotation questions

[Fields, Christopher J]

On Sep 29, 2014, at 6:02 AM, C. Titus Brown <ctb at msu.edu> wrote:

> On Sun, Sep 28, 2014 at 06:34:01PM -0500, Jessica Perry Hekman wrote:
>> Hi, Titus. I've been struggling with a de novo Trinity assembly for  
>> quite a few months now, and this weekend discovered your blog and the  
>> khmer protocols. I'm trying to apply them to my own process, and I have  
>> a fair amount of computing power locally, so I'm not running on an AWS  
>> server -- I'm hoping you're still willing to take a shot at some of my  
>> questions!
> 
> ...
>> * My system does not have formatdb for building the BLAST database, and  
>> when I went to install formatdb, I discovered that it is deprecated in  
>> favor of makeblastdb. However, apparently makeblastdb uses different  
>> parameters so I can't use your protocol with it exactly. I'm game to go  
>> try to figure out the change in parameter syntax between the two tools,  
>> but I'm curious why your protocol uses a deprecated tool. Should I be  
>> figuring out how to install formatdb instead of trying to make  
>> makeblastdb work?
> 
> The older BLAST is functionally equivalent to the later BLAST, and I'm
> pretty sure all of our code works for the older BLAST.  If and when we
> update we'll have to put some effort into validation.  So... short answer
> is that being conservative isn't always bad ;).

Just an aside, I think there is a simple script that comes with the last BLAST+ that will take older BLAST parameters and convert them for BLAST+.  No experience with it but it might be of some use.

Also, really cool to know there are others in Illinois working on really interesting projects using khmer!

>> Finally, thanks so much for all the work you've done to make RNA-seq a  
>> little easier. It has been quite the frustrating process so far.
> 
> Welcome -- and let us know how we can help!
> 
>> https://www.impactstory.org/jphekman
> 
> nice!
> 
> cheers,
> --titus
> -- 
> C. Titus Brown, ctb at msu.edu

chris