aligning the reads

[kjaja]

Hi,

I am planning to use CASAVA to align the reads to the reference genome using the fastq files. I was wondering if there are any quality control filtering steps that needs to be done before aligning the reads?

Thanks for your help

Kay

[GenoMax]

Kay,

If you are going to use the new version of CASAVA (v.1.8) you may need to remove the reads that would be normally filtered out before you do the alignments. See "dawe's" post on this page: http://seqanswers.com/forums/showthr...highlight=dawe

Illumina is supposed to come out with a update for CASAVA (http://seqanswers.com/forums/showthread.php?t=14316) that will do this automatically in October.