Yet another misassembly?
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- Posts: 67
- Joined: Sun Feb 04, 2007 10:23 pm
- Location: California Lutheran University, Thousand Oaks, CA
Yet another misassembly?
1492J04 also appears to be a misassembly. Although the initial assembly seemed to be okay, with one contig having both ends and not a lot of repeats, the restriction digests suggest that 1.7-2 kb are missing near one end. There is a repeat at the ends of 5/6 that seems to be missing reads in the middle, and contig 4 doesn't seem to fit (the fosmid end is at the left end of 5). Do you have more reads that might fix the problems?
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Re: Yet another misassembly?
After removing the assembly piece, incorporating all the additional reaction results, and re-running phredPhrap, the restriction digests suggests that there is an extra 2.4kb in the in-silico digests compared to the real digests:
After analyzing the high quality discrepancies and removing the unaligned high quality reads, I found a join between the two contigs that would resolve the misassembly:
Consequently, I do not believe that there are additional reads that are missing from the project.
After analyzing the high quality discrepancies and removing the unaligned high quality reads, I found a join between the two contigs that would resolve the misassembly:
Consequently, I do not believe that there are additional reads that are missing from the project.
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- Posts: 67
- Joined: Sun Feb 04, 2007 10:23 pm
- Location: California Lutheran University, Thousand Oaks, CA
Re: Yet another misassembly?
I forgot to suggest removing asmpiece and reassembling. Thanks.