asmpiece

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

asmpiece

Post by drevie » Thu Feb 09, 2012 8:27 pm

One of the fosmids we are improving is 1774P08. There is a "read" in the fosmid named 1774P08C19394asmpiece.a2 that extends pretty much through the entire fosmid-with uniform high quality peaks. I assume this is a fake read of some sort, but what is it doing there? Should we remove it?

Dennis

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

Re: asmpiece

Post by wleung » Thu Feb 09, 2012 10:03 pm

The fake reads that contain the suffix asmpiece correspond to assembly pieces that were used to guide the assembly process. The assembly pieces are derived from the consensus sequence in the original D. ananassae whole genome CAF1 assembly.

Because there are no major discrepancies between the real and the in-silico digests for 1774P08 (in all four restriction enzymes), I would recommend leaving the assembly piece in the Consed database and address the remaining inconsistent forward reverse mate pairs at the beginning of the clone separately.

== More detail explanation ==
Because some of the D. ananassae projects appeared to be highly repetitive (e.g. the red or difficult yellow clones), we decided to incorporate the consensus sequence from the CAF1 assembly into some of projects to help drive the assembly generated by phrap. The CAF1 assembly is based on the assemblies generated by the Arachne and Celera assemblers. Unlike phrap, these two assemblers utilize mate-pair information during the assembly process. Consequently, they tend to perform better than phrap when assembling highly repetitive regions.

There are two assembly pieces in the project 1774P08: 1774P08C19393asmpiece.a2 and 1774P08C19394asmpiece.a2. The gap between the two assembly pieces were filled by reactions called by Dr. Hauser's students last year. If the assembly pieces were removed from the project (and you reassemble the project with phrap), the project will consists of two separate contigs with more inconsistent forward-reverse mate pairs.

In general, we found that about half of the assembly pieces help with the assembly process. In cases where the assembly pieces are wrong, you can pull the assembly pieces out into their own contigs, change the bases to N's, save the assembly, and then re-run phredPhrap to create a new assembly without the assembly pieces.

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

Re: asmpiece

Post by drevie » Fri Feb 10, 2012 1:04 pm

Thanks for filling in the details about the fake reads.

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