[protocols] Eel-pond/annotation questions

[C. Titus Brown]

Excellent!  Thanks for helping us debug & find pain points -- much appreciated!

cheers,
--titus

On Thu, Oct 02, 2014 at 02:30:15PM -0500, Jessica Perry Hekman wrote:
> That was it. Restarted blastall...
>
> Jessica
>
> On 10/2/14 11:12 AM, C. Titus Brown wrote:
>> 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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>
> -- 
> Jessica P. Hekman, DVM, MS
> PhD student, University of Illinois, Urbana-Champaign
> Animal Sciences / Genetics, Genomics, and Bioinformatics
> https://www.impactstory.org/jphekman

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