How to obtain Contigs from cDNA Nanopore Sequencing

lbcb-sci / racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads

MIT License

197 stars 34 forks source link

How to obtain Contigs from cDNA Nanopore Sequencing #57

Closed jkbenotmane closed 3 years ago

jkbenotmane commented 3 years ago

Hi,

I am working with highly diverse Immune cell transcripts obtained from cDNA Nanopore Sequencing.

Would you have any advice on how to obtain the contigs needed for Racon from cdna Sequencing Data?

rvaser commented 3 years ago

Hi Jasim, unfortunately, I think that Racon won't be able to properly handle transcript data due to alternative splicing. You can try out https://github.com/ksahlin/isONcorrect.

Best regards, Robert

jkbenotmane commented 3 years ago

Okay understandable. Thank you ! :)