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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