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OpenGene / GeneFuse

Gene fusion detection and visualization
MIT License
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What is the minimum required read length? #10

Open billzt opened 6 years ago

billzt commented 6 years ago

I conducted a simulation. When my read length is 89bp, it outputs expected fusions. However when I use read length of 85bp. There are no results.

The main change is the LOG information: "sequence number before filtering: XXX". Shorter read length result in very few (or even zero) sequence number before filtering.

How do I adjust the source code to satisfy more shorter reads?

sfchen commented 6 years ago

Typically 100bp is required. 150bp PE data is preferred.

sfchen commented 6 years ago

https://github.com/OpenGene/GeneFuse/blob/master/src/indexer.cpp#L162