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Old 09-13-2011, 05:13 PM   #1
SES
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Default tracking Illumina read pair information

A number of assemblers (Velvet, Ray, Celera, ...) produce AMOS message files, but do any allow you to keep track of Illumina read pair information? I should emphasis that my question relates to viewing this information in Hawkeye, though it is also an open question. My understanding is that Hawkeye expects the pairs to be in a different orientation and this is part of the problem. I think the main problem is that this information is not even being tracked in the message file, at least this appears to be the case with Velvet (I have not tried the message files produced by Ray yet).

Anyone experienced (or solved ) this issue?
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Old 10-18-2011, 07:40 AM   #2
SES
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Default

Let me ask a slightly different question. How does Velvet credit a read to a contig and does this vary when using pair information?

Thanks.
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