[protocols] Eel-pond/annotation questions

[Jessica Perry Hekman]

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!

I'm doing RNA-seq with fox (Vulpes vulpes) which does not have a 
published genome or transcriptome, but which aligns very well against 
dog. Dog DOES have a published genome (fairly well annotated) and 
transcriptome.

I am happy to provide more details about my process so far, but in the 
interest of not writing an incredibly long introductory letter, right 
now I am trying to use your annotation protocol from eel-pond.

My questions:

* I see you are BLASTing against mouse protein. Since I have the closely 
related dog transcriptome, could I BLAST against that instead, and still 
expect to use your scripts /make-uni-best-hits.py and 
make-reciprocal-best-hits.py?

* 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?

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.

Jessica

-- 
Jessica P. Hekman, DVM, MS
PhD student, University of Illinois, Urbana-Champaign
Animal Sciences / Genetics, Genomics, and Bioinformatics
https://www.impactstory.org/jphekman