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 So

Genzyme Corp.

Functional Genomics

49 New York Ave.

Framingham, MA 01701



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