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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!
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!