<div dir="ltr">Any updates concerning the application to non-mouse databases?</div><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Aug 26, 2013 at 12:21 AM, Peter Fields <span dir="ltr"><<a href="mailto:pdf8z@virginia.edu" target="_blank">pdf8z@virginia.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">I've been working on the khmer protocols for RNAseq assembly and annotation protocol with a sample plant transcriptome (Silene latifolia). <div>
<br></div><div>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.</div>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br>********************************<br>Peter Fields<br>Graduate Student<br>043 Gilmer Hall<br>University of Virginia<br>Charlottesville, VA. 22904<br><a href="mailto:pdf8z@virginia.edu">pdf8z@virginia.edu</a><br>
<a href="http://people.virginia.edu/~pdf8z/">http://people.virginia.edu/~pdf8z/</a><br>********************************
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