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
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://galaxyproject.org