Question: Question about gene fusion
gravatar for mangfu100
4.7 years ago by
Korea, Republic Of
mangfu100680 wrote:


I have a question while i am reading a paper that is related to a gene fusion discovery.

below is some of the paper's content.

A paired end read will
be a member of multiple valid clusters as a result of homology
between genes, exon redundancy between transcripts, and the
multiplicity of valid clusterings. Fusion events are rare when
compared with the event of detecting a discordant paired end read
given the existence of a fusion event that would generate that read.
Thus we seek an assignment of each paired end read to a single
fusion event (valid cluster) that minimizes the number of fusion

(Valid cluster represents a potential fusion event implied by a set of discordant alignments)


i don't understand the bold text. I think the verb "minimizes" should be changed to "maximizes " because 

It maybe increase the number of gene fusion by calculating the single paired end read to a single gene fusion.


I hope you understand my basic questions  . I'm beginner in this field.

Anyway I am looking forward to your reply.

Thank you.

sequencing rna-seq alignment gene • 1.3k views
ADD COMMENTlink modified 4.7 years ago by Sean Davis25k • written 4.7 years ago by mangfu100680
gravatar for Sean Davis
4.7 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

The problem that the authors are trying to address is the problem of false positive results in the setting of reads that can map to multiple locations.  They are suggesting to use a heuristic that takes all the data available and seeks a minimal set of fusions from the set of all potential fusions.  So, I believe "minimizes" is what the authors meant.

ADD COMMENTlink written 4.7 years ago by Sean Davis25k

Thank you!

I appreciate a your answer and it gave me a insight to this field.

ADD REPLYlink written 4.7 years ago by mangfu100680
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