Another misassembly?

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drevie
Posts: 67
Joined: Sun Feb 04, 2007 10:23 pm
Location: California Lutheran University, Thousand Oaks, CA

Another misassembly?

Post by drevie » Fri Mar 02, 2012 8:16 pm

Project 2402D22 seems to have a misassembly on the right side. The assembly view is shown below. There are two sets of reads that are pointing in the wrong direction, contig 38 has both ends of the fosmid, and the restriction digests are off.

We tried tearing it apart (shown below). The reads are now all in the correct orientation, but the right end of the fosmid is not at the end. Checking restriction digests with various orientations and combos of the torn pieces shows about 1.8-2 kb are missing if 37c is not used. If 37c is used there are extra bands in silico. Maybe there are missing reads like other projects? Is 37c from the next fosmid? I'll note that the students made three primers off 37c and all failed.

Suggestions?
Attachments
2402D22-Misassembly.JPG
Misassembly
2402D22-Misassembly.JPG (33.63 KiB) Viewed 3823 times
2402D22-Misassembly-2.JPG
Misassembly and tear
2402D22-Misassembly-2.JPG (34.81 KiB) Viewed 3823 times

wleung
Posts: 185
Joined: Sun Feb 04, 2007 7:41 pm
Location: Washington University in St. Louis

Re: Another misassembly?

Post by wleung » Fri Mar 02, 2012 10:18 pm

Yes, there is a misassembly in the project 2402D22 and the project is missing a large number of reads. This is one of the projects that has been completed by a student in Bio 4342. The professional finishers at the Genome Institute were able to help us retrieve additional reads from the NCBI Trace Archive. The two sets of additional reads are available for download at the GEP 2012 Reaction Download Page under the section labeled "Additional traces from the NCBI Trace Archive."

drevie
Posts: 67
Joined: Sun Feb 04, 2007 10:23 pm
Location: California Lutheran University, Thousand Oaks, CA

Re: Another misassembly?

Post by drevie » Sat Mar 03, 2012 12:53 am

Great!

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