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What is the minimum required read length? #10

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tao-bioinfo opened this issue Mar 21, 2018 · 2 comments

tao-bioinfo commented Mar 21, 2018

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?

Member

sfchen commented Mar 21, 2018

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

Member

sfchen commented Mar 21, 2018

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

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