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

___________________________________________________________ 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 local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists, please use the interface at:

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

-- Jennifer Jackson http://galaxyproject.org