Contig ends internal-resolution?

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mburg
Posts: 1
Joined: Fri Jun 05, 2009 6:15 pm

Contig ends internal-resolution?

Post by mburg » Tue Feb 08, 2011 10:08 pm

Chris,

We have fosmid DMAC-13a that appears to have the fosmid right end within the end of the contig. Assembly view before tear is shown here:
DMAC-13 assembly view.png
DMAC-13 assembly view.png (28.53 KiB) Viewed 3123 times
After tearing at the predicted end of the contig and plaing the reads to the right in their own contig, all restriciton digests match. The new contig (4) is 1392 bases. Do we tag this and leave it? See new assembly view in second attachment:
DMAC-13a assembly view after tear.png
DMAC-13a assembly view after tear.png (31.08 KiB) Viewed 3123 times
The following is what the aligned window shows at the contig end prior to the tear....
DMAC-13 aligned reads.png
DMAC-13 aligned reads.png (79.91 KiB) Viewed 3123 times
Are these reads and sequence to the right from the next contig in the 'golden path'. If so, how do we check that??

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

Re: Contig ends internal-resolution?

Post by wleung » Wed Feb 09, 2011 12:59 pm

In cases where there are extra reads that extend beyond the fosmid ends, you can change all the bases after the fosmid ends to X's or tear the reads into a separate contig as long as there are no misassemblies in the region. In this case, the solution you have proposed is appropriate and you can confirm the tear with the restriction digests. If there are extra sequences that extend beyond the end of the fosmid, you should see a larger fragment than expected in the in-silico fragment compared to the real fragment. Please add a comment tag to contig4 that explains why you made the tear. You can also provide a more detail explanation in the finishing checklist under the item: "Comment tags on any contigs over 2kb that are not in the assembly".


> Are these reads and sequence to the right from the next contig in the 'golden path'. If so, how do we check that??

You can search the whole genome (CAF1) assembly is at the FlyBase BLAST service. Hence you can use the consensus sequence from contig3 and contig4 and perform a BLASTN against the D. mojavensis CAF1 genome assembly to verify that the extra sequences are from the golden path.


From the screenshot of the aligned reads window, it appears that the clone end tag is on the read. Please remove the clone end tag from the read and add the clone end tag to the consensus.

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