Inquiry Regarding Detection of Read-Through Gene Fusion Events Using EasyFuse

[Zeyu618]

Dear EasyFuse Team,

I hope this message finds you well. I am currently utilizing EasyFuse for fusion transcript detection in paired-end RNA-seq data and am interested in identifying read-through gene fusion events. Could you please advise if there are specific parameters or configurations within EasyFuse that facilitate the detection of such events? Any guidance or recommendations you can provide would be greatly appreciated.

Thank you for your assistance.

Best regards,

Zeyu

[RitzelC]

Dear Zeyu,
if you are interested in read-throughs you could use the cis-near fusion classification of easyfuse to identify GFs on the same stand and same chromosome. There is also a parameter --cis_near_dist (default: 1000000 / 1 Mb ), which defines the maximum distance of two breakpoints to be classified as "cis_near". You could modify it in the 04_joint_fusion_calling module to adjust it to your needs.

Does this answer your question?

Best regards,
Christoph