More sequncing checklist questions

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mshaw
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Joined: Sun Feb 04, 2007 10:26 pm

More sequncing checklist questions

Post by mshaw » Fri Mar 30, 2007 8:49 pm

There are several items that we don't understand/know how to do.
1). What are "PCR only regions" and how do we find them?
2) What does "assembly pieces used" mean?
3) how do we "run findit"?

cshaffer
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Location: Washington University in St Louis
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final checklist

Post by cshaffer » Fri Mar 30, 2007 10:18 pm

PCR only regions are regions where the only template is PCR product. Since all your reactions were done on fosmid template you have no PCR only regions.

Assembly pieces are some times used to help phrap assemble difficult regions. They are usually generated from regions of overlap with adjacent clones that have already been finished (no reason to solve a difficult region twice so just bring in the correct sequence and have phrap align all the reads to the "assembly piece"). As far as I know no one used assembly pieces.

FindID is a Genome Center specific program to screen for transposons and other areas that might be putative contamination. You don't need to run this you can just run the BLAST and see if you pick up any suspicious regions.

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