We used the generate pileup tool with consensus base calling option
Maq with default options. In the output, the quality scores of the
were changed. For example if the input score of bases in the SAM file
'IIJIH'. They were changed to '22321'. Is this a glitch or is this
expected? Thank you.
Sorry for the delayed reply. Are you still having problems with
This isn't correct behavior - quality scores should be unchanged,
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
Please state in your email the input/output dataset #s and which
you believe to be the quality scores in the input SAM dataset and