I have two questions regarding gene fusion:
1) are there existing tools that can simulate gene fusion rna-seq reads?
2) how to determine the fusion gene allele frequency based on rna-seq reads? by which, I mean, for example, if we want to determine the variant allele frequency for a SNV, I just need to count the number of reads covering this nucleotide and have the mutated base, divided by the total number of reads that cover this base; then, for gene fusion, how to do a similar calculation? or is there even such measures for gene fusion? The reason I asked was because, I want to determine a lower limit for reliable detection. For example, in a heterogeneous tumor sample, only 10% of the cells have a fusion gene, then, would the pipeline/tool be able to detect this fusion gene in this sample? and how to quantify such low limit?
Thanks!
For 1) there's a tool called fusim by Andrew Bruno et al. (see the attached links). I haven't been able to test it yet, but it should be exactly what you want.
http://www.biomedcentral.com/1471-2105/14/13
https://github.com/aebruno/fusim
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Bioinformatics
- Bioinformatic Tools