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Old 06-11-2012, 06:49 AM   #1
Khaz
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Location: Ann Arbor, MI

Join Date: Apr 2012
Posts: 1
Default TopHat Fusion: -r parameter sensitivity

I am running TopHat (2.0.0) on RNASeq data with the goal of locating gene fusions and was wondering how sensitive TopHat is with respect to the -r (insert size) parameter when determining fusions. I have seen threads discussing this parameter, but not with respect to fusion calling.

The RNASeq data is coming from Illumina HiSeq experiments, and insert seems to vary from ~150 to ~300 with very large std-dev (up to 1000s of bp). This is according to samstats when reads are mapped to the genome. The reads are paired, 50bp each.

Since I am running TopHat on many files in parallel, pre-computing the insert size statistics is an expensive step that I would like to avoid. I am hoping that setting the -r to a constant value and defining a large -insert-std-dev could avoid tweaking the -r on a per-sample level. In several trial runs, changing the -r parameter for samples with seemingly large mean insert sizes resulted in no changes to the filtered fusions reported.

Given these observations I was wondering how important is getting the -r right versus setting the std-dev higher and how exactly TopHat uses the -r parameter in the context of finding fusions.

Any information on the above would be much appreciated. Thanks!
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