Dave,
The fact that the Tophat wrapper was not setting the genome based on
the alignment genome was actually a bug, but I just fixed it in
changeset 5570:0c1251f25c6b.
Let us know if you have further questions.
Regards,
Kelly
On May 17, 2011, at 10:57 AM, Dave Walton wrote:
I'd like to get a better understanding of the point of the database/
build
attribute, and pose the question of when is the appropriate time to
have it
set?
In our case at the Jackson Laboratory, the most common build is
NCBI37/MM9.
However, the feeling of many folks here, is that this should not be
set on
our fastq files. The only place we really run into trouble is with
cufflinks. If you haven't set the db when you get to cufflinks
you'll get
an error.
Our suggestion is that there should be one of two options:
1) Tophat has the ability to set the database of the output files
based on
the genome that was selected for alignment.
2) There should be a module that can be plugged into a workflow
that would
set the database of the file prior to passing the file to cufflinks
(or any
other two that requires the database attribute to be set).
We are curious if anyone else is running into this issue, and how it
is
being solved.
We're thinking about hacking the Tophat wrapper, but I wanted to
check with
others before I did this.
Thanks,
Dave
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