Re: [galaxy-user] Maq consensus calling changes quality score of the read?

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

[galaxy-user] Maq consensus calling changes quality score of the read?

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 expect

[galaxy-user] Maq consensus calling changes quality score of the read?

Hi, We used the generate pileup tool with consensus base calling option using Maq. 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