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Scott,<br><br>
I decide to take an "easier" approach as a start - I will try
to load NCBI and UCSC cattle genomes to GBrowse. Once that works, I
can move on with more customized data sets.<br><br>
I have following questions in doing that:<br><br>
1.<br>
A technical one: When I try to load a cattle chromosome using your
'load_genbank.pl', I got a memory problem (there is 8 GB RAM on the
machine - I bet there must a work around?)<br><br>
> load_genbank.pl --create -dsn dbi:mysql:gb_cattle -user --pass
--accession NC_007320<br>
Loading NC_007320...<br>
Out of memory!<br>
Out of memory!<br>
Out of memory!<br>
Segmentation fault (core dumped)<br><br>
2.<br>
Can I load all chromosomes into one database? Or should I create
separate databases for each chromosome? (I assume the former but not
sure).<br><br>
3.<br>
If I also bring in UCSC golden tracks, should I set up a different
database, Or can I put them into one db, naming UCSC chromosomes a little
differently?<br><br>
Thank you,<br><br>
Zhiliang<br><br>
<br>
<font color="#808080">--<br>
Zhi-Liang Hu (PhD)<br>
Associate Scientist,<br>
Department of Animal Science,<br>
Center for Integrated Animal Genomics,<br>
National Animal Genome Research Program,<br>
Iowa State University<br>
Tel: 901-759-0643<br>
Mob: 901-212-2820<br>
Web:
<a href="http://www.animalgenome.org/" eudora="autourl">
http://www.animalgenome.org<br><br>
</a></font><tt><font face="Comic Sans MS" color="#808080">"Not
everything that counts can be counted, and<br>
not everything that can be counted
counts."</font></tt><font color="#808080"><i> </font></i></body>
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