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Old 11-19-2010, 07:28 AM   #1
Junior Member
Location: denmark

Join Date: Apr 2010
Posts: 8
Default BWA mapping fastq files with Illumina quality


I am still new in these matters, I was told to map illumina reads to the human genome. I was given the fastq files and proceeded to use BWA, everything ran smoothly 'til today when I realised the reads I had mapped had the Illimina base qualities instead of Sanger's . This raised several questions: Why can BWA map fastq files with the Illumina instead of Sanger? What are the consequences of this?? Unmapped reads?? miscalled variants?? I am pretty concerned since the mapping took around two weeks and I am not sure if I need to start from scratch again and remap the fastqs in sanger format. Please, any help will be highly appreciated!!


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