Finishing checklist questions

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cjones
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Location: Moravian College, Bethlehem PA
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Finishing checklist questions

Post by cjones » Tue Mar 20, 2007 7:07 pm

I'm finishing my finishing as it were, and going down the checklist. When I tag the "cloning ends," does that mean to tag the consensus sequence rather than the flanking vector sequence? How many bases should be tagged, just the terminal one?

To check for N's in the consensus I ran search for string, and it gave me hits at every base from position 478 to 499, as well as 504. But in the consensus itself, both exported and within consed, those positions are all valid (non-N). So I'm ignoring the "search for string" results, but any idea why it's happening?

For adding my name, where do I append the "left end comment tag"? At the left end, I know, but how many bases do I include, and is it the left end of the consensus or of the entire contig (including vector sequence, which is now all X's)?
Chris Jones
Assoc. Prof. of Biology
Moravian College
Bethlehem PA

cshaffer
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Location: Washington University in St Louis
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adding end tags and comments

Post by cshaffer » Tue Mar 20, 2007 7:50 pm

There is no set standard for how many bases to tag for the clone end and comment tags. I personally like to do several because I sometimes find it difficult to see tags of only one base. So I always suggest that students pick at least 4 or 5 bases so it’s easy to see.

Also the precise position does not matter. Usually there is an easily identifiable transition from vector to insert but on these whole genome shotgun assemblies you only see this if you specifically order primer to read off the end of the insert and into the body of the vector. I would just put the tag at or very near the first high quality bases and ignore the low quality ends.

I have never seen the disappearing N problem with search for string; I guess my only question here is it happening to only one project or all your projects?

cjones
Posts: 99
Joined: Sun Feb 04, 2007 10:19 pm
Location: Moravian College, Bethlehem PA
Contact:

Re: adding end tags and comments

Post by cjones » Thu Mar 22, 2007 5:40 pm

cshaffer wrote:I have never seen the disappearing N problem with search for string; I guess my only question here is it happening to only one project or all your projects?
Just mine, apparently; the only other student who gets a non-empty return from using "n" in search for string actually does have n's at the indicated positions.
Chris Jones
Assoc. Prof. of Biology
Moravian College
Bethlehem PA

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