[protocols] Eel-pond/annotation questions

[C. Titus Brown]

Hmm check to make sure -p T was spec

---
C. Titus Brown, ctb at msu.edu

> On Oct 2, 2014, at 11:57, Jessica Perry Hekman <hekman2 at illinois.edu> wrote:
> 
>> On 10/02/2014 06:18 AM, C. Titus Brown wrote:
>> 
>> The problem here is that all of the commands expect a protein database, and
>> BLAST treats DNA and protein databases quite differently.  (I'm also not sure
>> the cutoffs or the scripts I've provided will work with DNA databases.)
>> The easiest thing to do might be to grab the dog proteome, which should
>> be available alongside the transcriptome somewhere -- at least, UCSC
>> should make it available...
> 
> You'd think that would have occurred to me, but it didn't!
> 
> It was indeed right next to the dog transcriptome. I got it. formatdb was a little irritable about it:
> 
> 
> [formatdb] WARNING: Sequence number 42467 (gi|5835665|ref|NP_008483.1|CYTB_15041), 158 illegal characters were removed:
> 6 Es, 28 Fs, 38 Is, 58 Ls, 22 Ps, 6 Qs
> 
> (etc, for every sequence so far as I can tell). Something to worry about?
> 
> Anyways, I am re-running blastall now. Thank you.
> 
> Jessica
> 
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