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
On 3/14/12 1:54 PM, Antony Jose wrote:
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.
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