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Posted: Wed Feb 26, 2014 1:37 am
Several students have what appear to be missassemblies that are indicated by blocks of HQD flanked by blocks of aligned sequence.
We are tagging these as possible misassemblies, but I really want to rip those reads out.
Since no restriction map, my understanding is to leave them in - correct?
Posted: Wed Feb 26, 2014 2:31 am
Yes, your students do not need to resolve the misassembled regions unless they are near gaps or contains low quality data. You can simply add a comment or "doNotFinish" tag to regions that might contain a misassembly.
Because of the small number of paired end reads with large insert sizes and the lack of restriction digests, in most cases there is insufficient data to resolve a misassembly. Consequently, resolving misassemblies is not a goal of the GEP sequence improvement project.
However, if you would like to try to resolve the misassembly, the GEP Hybrid Assembly Walkthrough
contains an example (beginning on page 18) that illustrates how you can use the Illumina reads to help resolve a misassembly.