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Hi!
I am a graduate student at Yale and am assembling shotgun sequence from BACs using phred/phrap/consed. I am currently about to start finishing using autofinish. I am using the standard St. Louis read-naming conventions. I understand how to make autofinish run and how to interpret the output, but have three questions.
(As a disclaimer, I have read--and re-read--the consed documentation and original papers and done numerous web searches to try to find answers but have had no luck so far. If these are "stupid questions" and the info is already out there or in the documentation, please point me in the right direction so I can figure it out on my own. I'd be very grateful!)
My first question concerns how to name the reads that autofinish tells me to create. For example, say autofinish tells me to repeat a universal forward primer read. The original forward read is named something like READ.b1. What do I name the repeated read? I assume READ.b2, but that might be wrong.
Question 2: If autofinish tells me to do a primer walk with a custom primer, I understand that it should be named "READ_1.i1" I assume that the number after the underscore the number of the primer that autofinish designed, but again I could be wrong.
Question 3: How do I add the new reads to the existing assembly? Do I use the new reads that autofinish told me to make using the "Add New Reads" function in consed? If so, do I need to do anything special to ensure that the next time I run autofinish, it knows that the reads it previously suggested I creat have been added?
Thank you in advance for your time!
Matt Nicotra
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