Unclear problem with 1774P12

Ask questions about sequence improvement / finishing D. mojavensis projects here.
Post Reply
drevie
Posts: 67
Joined: Sun Feb 04, 2007 10:23 pm
Location: California Lutheran University, Thousand Oaks, CA

Unclear problem with 1774P12

Post by drevie » Tue Mar 20, 2012 6:55 pm

For 1774P12, there are two contigs with a gap estimated to be 300 bp, but all of the reads appear to be consistent. However, the restriction digests are consistently off at each end of the fosmid. Any suggestions?
Attachments
1774P12-problemAV.JPG
1774P12-problemAV.JPG (52.66 KiB) Viewed 3479 times
1774P12-problem.JPG
Restriction digest
1774P12-problem.JPG (75.38 KiB) Viewed 3479 times

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

Re: Unclear problem with 1774P12

Post by wleung » Wed Mar 21, 2012 8:31 pm

I believe the discrepancies are caused by multiple misassemblies in the assembly pieces. After removing the assembly pieces, incorporating all the reaction results and additional gap traces, and re-running phredPhrap, both the discrepancies at the fosmid ends and the gap appeared to be resolved.
1774P12_asm_after_added_reads.png
Resolve misassembly in 1774P12
1774P12_asm_after_added_reads.png (124.26 KiB) Viewed 3476 times

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

Re: Unclear problem with 1774P12

Post by drevie » Thu Mar 22, 2012 12:35 pm

Thanks. It looks like the asmpiece files have been throwing us off.

Post Reply