Bioinformatics Asked by beachwildernessgene on August 10, 2021
I want to use rna seq data to later perform functional tests on fusion genes.
so before that I need to filter the "best results" (of rnaseq) for deciding which candidates I actually want to try in the lab.
one criterium is the split read. (among coverage, discordant mate and confidence)
In some cases the split read (or discordant mate/coverage) of one of the two genes that fusioned is "0".
Does that automatically mean that the gene is no longer a candidate for functional testing?
Unfortunately I only got the results in an excel data sheet and don’t know which tool was used to gain data.
For discordant mapped reads, a position of 0 for the pair of a mapped read usually means that the pair couldn't be mapped anywhere. This would be expected for fusion events because some reads could originate from across the fusion site (i.e. not being fully contained in either "unfused" gene), leading to a sequence that doesn't match anything in the reference.
Answered by gringer on August 10, 2021
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