Interpretation of output spanning reads and discordant reads

[ashleyzhou972]

I was wondering if there's a more detailed description of the output columns,
The only resource I could find was here: https://university.stjude.cloud/docs/genomics-platform/workflow-guides/rapid-rnaseq/#interpreting-results, and the FusionEditor help page. Neither of those resources contain definitions for columns such as matchA, repeatA, coverageA, or ratioA.

Specifically, I have the following questions:

• If the readsA and readsB columns in final_fusions.txt are columns containing number of chimeric reads for a fusion, why are the two having different values for the same fusion? By definition a chimeric read should contain sequences from both A and B genes.

• Are there metrics equivalent to star-fusion's JunctionReadCount and SpanningFragCount columns? According to STAR-Fusion wiki, the former "indicates the number of RNA-Seq fragments containing a read that aligns as a split read at the site of the putative fusion junction", and the latter "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".

If you could illustrate how CICERO's output readsA and readsB columns (or maybe other columns) relate to these two concepts, to enable us to do a more thorough comparison of the two methods, that would be great!

Thank you!

[adthrasher]

The FusionEditor has a link to the file format. @liqingti - Can you answer the questions about the read counts?

[adthrasher]

I believe that readsA indicates reads that were originally aligned at posA. So it is based on the original number of aligned reads at each breakpoint.

[ahdee]

@adthrasher were you able to get any more info? I second this question. It would be valuable to have both the junction and discordant reads, the reason is because it allows a way to calculate relative abudance when normalized to the library.

[liqingti]

Q1: readsA and readsB stands for "number of junction reads that support the fusion at breakpoint A / B".
For most cases, it equals the number of supporting soft-clip reads at each breakpoint.

Q2: basically JunctionReadCount in STAR-Fusion approximately equals readsA+readsB in CICERO. We do not have similar output of "SpanningFragCount" in CICERO.