STAR-Fusion: Problem in interpreting

Question

[Ranan Jyoti Sarma]

Hi RNA-seq community

Could anyone give me an idea about these two terms "JunctionReadCount" and "SpanningFragCount" of STAR-Fusion result?

For some fusion, these numbers are very high (More than 100) and for some fusion, the numbers are extremely low (Less than 20). In this case, is there any threshold for filtering out the fusions having lower JunctionReadCount and SpanningFragCount?

Answer 1

[lakhujanivijay]

HI Ranan Jyoti Sarma

The JunctionReads column indicates the number of RNA-Seq fragments containing a read that aligns as a split read at the site of the putative fusion junction.

The SpanningFrags column indicates the number of RNA-Seq fragments that encompass the fusion junction such that one read of the pair aligns to a different gene than the other paired-end read of that fragment.

Source: https://github.com/STAR-Fusion/STAR-Fusion/wiki

Please read throught this page in details for more information.

[LayneSadler]

My takeaway is that the JunctionReads is higher confidence because the fusion is actually observed.