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-   -   How to detect real deletion or gaps in sequencing projects (http://seqanswers.com/forums/showthread.php?t=451)

watashi 08-01-2008 02:15 PM

How to detect real deletion or gaps in sequencing projects
 
Dear all

We have 3 genomes sequenced of 11, 15 and 23 fold coverage by 454 Sequencer. At least more than 10kb of the gap regions (defined by unsuccessful reference mapping) are coding regions containing little repetitive sequences. Interestingly, these gap regions appear quite concordantly among the 3 genomes.

Would anybody know how to utilize the scaffold files or related in order to check whether they are real gaps or not? Automation cannot be done if the process has to be studied by manually comparing the results generated by reference mapper and de novo assembler.

_________ ................ ________
|..............|................|..........|
|.ATTTCC..|---------->| CGCCC |
|_________|................|______|

Say, in reference genome, it is:
ATTTCCTTAGGAACGCCC

can we have a quick way to identify ATTTCCCGCCC (not to do that manually…) so to confirm the genome has deletion of (TTAGGAA) or not?


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