Question: Question About Galaxy
0
Jennifer Hillman Jackson ♦ 25k wrote:
Hi Qianli,
It looks as if you are using the Extract DNA tool? GTF/GFF files have
coordinates with a 1-based start position - and this was your input,
but
the output from this tool produces coordinates with a BED-style
0-based
start position.
The genome index files used by the tool are in .2bit format and the
source is encoded into the full name. The sequence content of the
reference genome is not altered by the tool. Perhaps the
interpretation
of the coordinates is the source of the difference or you are sourcing
a
different version? If you have a question about where we sourced a
genome, please let us know.
To see a quick description of both BED and GFF format together in the
UI, click into the tool "Convert Formats -> GFF-to-BED converter". For
more in-depth descriptions, please see our wiki:
http://wiki.g2.bx.psu.edu/Learn/Datatypes
Next time, please send questions directly to our mailing list, with
the
"to" address as galaxy-user@bx.psu.edu.
Best,
Jen
Galaxy team
--
Jennifer Jackson
http://galaxyproject.org