Contig end question

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bdanner
Posts: 6
Joined: Sun Jan 08, 2012 3:21 pm

Contig end question

Post by bdanner » Wed Feb 01, 2012 9:16 pm

We are wondering where to call the ends on contig5-1041G20. At the left most end we see a lot of X's which signifies a vector in two of the reads and are wondering if we should call the end there. On the right most end we see X's in the reads as well and are wondering if we have the correct placement of the vector end tag.




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

Re: Contig end question

Post by wleung » Wed Feb 01, 2012 11:40 pm

The fosmid end reads in the project have the prefix fosmidend. The fosmid end reads has the following naming convention:
fosmidend<sequencing_center><project name>.<orientation>1

<sequencing_center>
ac = Agencourt
wgc = Washington University Genome Institute

For example, the fosmidendwgc1041G20.g1 trace would correspond to a reverse fosmid end read for the project 1041G20 generated by the Washington University Genome Institute.

In the first screenshot, the clone end tag in the second read should be removed. In the second screenshot, the clone end tag should be placed on the consensus A at position 115.

bdanner
Posts: 6
Joined: Sun Jan 08, 2012 3:21 pm

Re: Contig end question

Post by bdanner » Wed Feb 08, 2012 12:50 pm

Thanks a bunch Wilson!

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