[protocols] blastall and make-reciprocal-best-hits.py with TAIR10

[Peter Fields]

Any updates concerning the application to non-mouse databases?


On Mon, Aug 26, 2013 at 12:21 AM, Peter Fields <pdf8z at virginia.edu> wrote:

> I've been working on the khmer protocols for RNAseq assembly and
> annotation protocol with a sample plant transcriptome (Silene latifolia).
>
> In place of the mouse refseq, I attempted to use the TAIR10 refseq (after
> running the standard mouse refseq protocols). I found very strange outputs
> using the TAIR refseq database, TAIR10_pep_20101214. Specifically, an
> attempt to identify orthologous sequences was completely unsuccessful
> (essentially blank file). And then identifying names for sequences in the
> current pipeline isn't possible. This seems to result from the mouse refseq
> focus of the eel-pond scripts. Not a problem, just something that might be
> generalized in future updates.
>
>
>
>
>


-- 
********************************
Peter Fields
Graduate Student
043 Gilmer Hall
University of Virginia
Charlottesville, VA. 22904
pdf8z at virginia.edu
http://people.virginia.edu/~pdf8z/
********************************
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