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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