Hi Antony, Sorry for the delayed reply. Are you still having problems with Pileup? This isn't correct behavior - quality scores should be unchanged, which means they are most likely Phred33+. Can you reproduce this on the public main Galaxy instance now (Samtools has been updated since your email was originally sent - however, this was never a known issue)? If still reproducible, please share a link to a history containing the inputs and output datasets (all undeleted), as generated on the public main Galaxy instance, and we can take a look. Use "Options (gear icon) -> Share or Publish", generate link, and email that back to me directly. Please state in your email the input/output dataset #s and which columns you believe to be the quality scores in the input SAM dataset and output Pileup dataset. Best, Jen Galaxy team On 3/14/12 1:54 PM, Antony Jose wrote:

Hi, We used the generate pileup tool with consensus base calling option using Maq with default options. In the output, the quality scores of the bases were changed. For example if the input score of bases in the SAM file were 'IIJIH'. They were changed to '22321'. Is this a glitch or is this expected? Thank you. Antony

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