Restriction Digests after Adding New Reads

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gkuleck
Posts: 3
Joined: Sun Feb 04, 2007 10:21 pm

Restriction Digests after Adding New Reads

Post by gkuleck » Wed Mar 21, 2007 3:04 am

I put in new reads and edited my finishing project. After I placed the frag.txt into the edit_dir. After entering the pathway for the allContigs.fasta there is this error message:

Vector data in
/Users/student4342/Desktop/215-F05/edit_dir/allContigs.fasta must just be acgt's, but intstead contains
>contig2./215-f05.fasta.screen .ace.10(wholecontig)
Could there be more than one vector in this file?
There shouldn't be.

I tried to write all contigs in fasta file, save and open Xterm again. This did not change. Could this be the result of the new reads which revealed vector within my contig?

Nicole Yu

cshaffer
Posts: 211
Joined: Sun Feb 04, 2007 10:29 pm
Location: Washington University in St Louis
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file for digests

Post by cshaffer » Wed Mar 21, 2007 3:26 pm

The file you want to point to is not the contigs but the file with the sequence of the vector backbone. Consed already knows the sequences of the contigs but it needs to add in the vector sequence to get the complete sequence of the circular fosmid before it can cut it in silico. This file has a special format where the sequence starts and ends with the insertion site.

Note that the algorithm that tries to guess the orientation of the insert with respect to the vector is not very smart and is having even more difficulty with these whole genome mini libraries don't be surprised if the in silico digest adds two cut sites at the insert/vector boundary or if it gets the orientation wrong. If it gets the orientation wrong there is a button in the digest viewer to compl(ment) vector. If it adds two cut sites at the insert vector boundary you can look at the text description of each band and figure out which two bands need to be added to get the correct predicted size.

The name of the file with the vector is pCC01.fasta, which should be in your edit_dir. So based on your apparent path from the error message you would change the vector path to (not sure about case):

/Users/student4342/Desktop/215-F05/edit_dir/pCC01.fasta

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