Hello Kathy,
To confirm, this was run on the public Main Galaxy instance at
https://main.g2.bx.psu.edu/ (usegalaxy.org ?).
It could be that your intervals are overlapping with a gap region (a
known gap, padded with "N's" - there are are several classes). This
could be quickly checked by viewing the track in the UCSC Genome Browser
with the "Gap" track set to full and the "Assembly" track set to dense
(everything else set to "hide", if you want). Zoom out as necessary.
If you are still not sure, please share your history with me and I can
provide feedback. Either generate a share link or add me as a share user
and email me back. Use "Options (gear icon) -> Share or Publish".
Best,
Jen
Galaxy team
On 7/24/12 11:49 AM, So, Kathy GZ/US wrote:
Hi,
I’m having trouble with the Generate Pileup tool and hope that you could
help me troubleshoot this. I ran the tool successfully with the
following options:
* Use built-in index
* Print the mapping quality as the last column
* Print all lines
* Cap mapping quality = 60
* Call consensus = yes, then default parameters
The reference bases of the entire pileup file, however, are all “N.” I
double checked and the all the files have the same reference genome
(mm9). Do you have any ideas on what went wrong?
Thanks very much for your help,
Kathy
Kathy So
Genzyme Corp.
Functional Genomics
49 New York Ave.
Framingham, MA 01701
508-271-4717
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___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
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