Is It Possible To Perform De Novo Assembly Of Specific Regions Of Human Genome?

Question

[mazzottidr]

I've been asked if it is possible to reassemble a specific region of the genome that is poorly covered in most-used human genome assemblies. A collaborator performed series of experiments and identified a possible isoform of a specifc receptor that is located in a preicentromeric region poorly covered in the human genome assembly. However, to validate that (since when BLASTing this region nothing comes up), we though about reassembling the genome of this specific region. We have exome sequencing data. Reference alignment only produced missense variants in the annotated parental isoform. Is it possible to reassemble this region in order to find crypt evidence for this another isoform using my exome data? Thanks in advance!

[deanna.church]

Have you checked this against GRCh38 or just GRCh37? In general, regions not well covered in the reference are hard to assembly- but there is significant improvements in GRCh38 in the pericentromeric regions.