"?" characters from HiSeq FastQ affecting Mira: HELP!!!

[alanmcn1]

Hi everyone

I am currently working on my 1st ever set of HiSeq data. I normally use Mira to run mapped assemblies with Illumina data, but am hitting problems with my new HiSeq data. Mira is finding lots of "?" or ASCII code 63 characters and is failing to assemble. Can anyone advise if they have hit this problem and/or they found a solution?

many thanks

Alan

[fkrueger]

HiSeq instruments run with the latest control software will produce Sanger encoded FastQ files (Phred + 33), so a '?' means a Phred score of 30. Did you maybe specify to use the 'old' Illumina 1.3+ encoding?

[alanmcn1]

Thanks for quick reply, and that makes lots of sense. Am not sure how i would adjust Mira to handle this data?