FUSION_CDS and FUSION_TRANSL sequences

17 views

Skip to first unread message

Francisco

unread,

Nov 28, 2025, 10:56:04 AM11/28/25

to Trinity_CTAT_users

Hello,

Thank you for developing this useful tool.

I have a question regarding the sequences that appear under FUSION_CDS and FUSION_TRANSL columns when running CTAT-lr-fusion. Are these sequences derived from the sequences of the input reads or are they generated based on the predicted breaking point and the reference sequences of the two genes involved in the fusion?

Thank you in advance,

Fran

Brian Haas

unread,

Nov 28, 2025, 12:16:42 PM11/28/25

to Francisco, Trinity_CTAT_users

Hi Fran,

This part is just taking into account the fusion breakpoints and the reference annotations. You can use StringTie to assemble the isoforms based on the fusion contigs and then examine the predicted coding sequences. We haven't implemented that part of the process yet into ctat-lr-fusion, but it'd make sense to do so for a future release.

--
You received this message because you are subscribed to the Google Groups "Trinity_CTAT_users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to trinity_ctat_us...@googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/trinity_ctat_users/63b538bc-2c16-4344-9da0-1cc5a8d2d249n%40googlegroups.com.