search

OpenGene / GeneFuse

Gene fusion detection and visualization
MIT License
114 stars 62 forks source link

Whether the software supports fastq data from both DNAseq and RNAseq or not? #5

Open xiezhan opened 6 years ago

xiezhan commented 6 years ago

Can I use this soft to call fusion gene from RNAseq data? Could anyone give me some advice?

thanks so much !

sfchen commented 6 years ago

This tool is originally designed for detecting fusion from DNA-Seq data.

Theoretically it can be used for detecting fusion from short reads (Illumina / Lifetech etc) RNA-Seq data. But I haven't done a lot of testing.

False negative may happen in such case: the fused exon is too short, and its neighbour intron is too long.

For long reads RNA-Seq (PacBio / Nanopore etc) RNA-Seq data, please use other tools.