(I am not part of the galaxy team)

On Oct 14, 2011, at 8:33 AM, Marcin Jakalski wrote:
The third issue is with the "Reverse Complement a MAF file" tool. ... the coordinates change, meaning, tool starts counting from the end position of a chromosome, not from the start position. ... I think it would be better if the tool would keep the original coordinates.


I can't comment on your first two issues. But for the third one, FWIW, keeping the original coordinates would produce a file that is no longer correct according to the definition of the MAF format, which can be found here:
        http://genome.ucsc.edu/FAQ/FAQformat#format5

So to do that I need to take the length of chromosome and subtract the start position from it, then subtract length and only then I get the same coordinate as in my set of intervals.

This is the reason why the MAF format carries the chromosome length on every line.

Someone could make a tool that does it the way you suggest. Hopefully they wouldn't call the result MAF.

Bob H
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

 http://lists.bx.psu.edu/

Reply via email to