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alexdobin / STAR

RNA-seq aligner
MIT License
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Minimal RNA-seq requirements for chimeric reads for STAR-fusion #1412

Open keremw opened 2 years ago

keremw commented 2 years ago

Hi, I want to sequence to see differences in the fusion rates. I understand reads need to be paired-end? And what length is advised? Would 50 reads on each side suffice? Or would I need longer reads? Also what depth each sample needs to be sequenced? Would the Encode minimal 20M reads be enough? Or for this question is a deeper sequencing needed? Thanks, Kerem

alexdobin commented 2 years ago

Hi @keremw

fusion alignment is more error-prone than normal, so you would want longer paired-end reads. I would recommend at least 2x100b. As to sequencing depth, it depends on the expression levels of fusion transcripts, so it's not easy to predict. The more the better, of course... :)

Cheers Alex