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Old 08-12-2008, 07:28 AM   #19
NGS specialist
Location: Malaysia

Join Date: Apr 2008
Posts: 249

This is an area we're trying to perfect at the moment. Basically you gotta know that novoalign mapping quality scores are meant to be as close to maq mapping qualities as we hope to get. Therefore scaling may not be necessary if we can show that low quality novoalign mapping qualities are the same as those for maq , and vice versa for maq.
The .map file is the key here because it contains this information and we're neglecting these by using eland format Therefore it's crucial for us to go from the text format in novoalign to the maq format whilst keeping all that useful information.
The good news is that because we're mapping more with novoalign you have more SNPs being called. We hope to have this format conversion with quality scores ready by next week.
Perhaps you can send me a private msg and I can provide you with some charts showing how these mapping qualities compare between novoalign and maq??
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