About "INTRACHROMOSOMAL"

[小林賢子]

Dear Dr. Haas

Always thanks your response.

Let me ask another question.

The other day you told me about “INTRACHROMOSOMAL” in the STAR-Fusion annot, as follows,

"These annotations are based on the gene coordinates and not part of the fusion lib." 

I think that intrachromosomal cases include inversion and deletion. Strictly speaking, however, there are cases of translocation between alleles rather than inversion or deletion. For example, as there are inv(16) and t(16;16).

Is it true “INTRACHROMOSOMAL” with this distinction (excluding translocation between alleles) in the STAR-Fusion annot?

Tetsuko Kobayashi

[Brian Haas]

The INTRACHROMOSOMAL with NEIGHBORS are the suspicious ones. If there’s a rearrangement then you’ll have other annotations showing up too, accordingly. Deletions will have larger intergenic distances 

--
Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas

 

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