How to combine the liftoff and RNA_seq

[ld9866]

Dear Liftoff: Thank you so much for developing such good software for us to use. We are annotating a genome, and as we know our similar genome has well-annotated files, we would like to use your software to fully use the published annotation files. At the same time, we also measured the second-generation transcription and third-generation transcription of some tissues, hoping to annotate some genes that have not been fully annotated. Would you like to tell me if we have any good ways to combine them? Looking forward to hearing from you! Have a good day！

[agshumate]

Hi, my reconmondation would be to use StringTie --merge (http://ccb.jhu.edu/software/stringtie/index.shtml?t=manual). if you have assembled your RNA-seq data and have it in gff/gtf fomat, you can provide this to StringTie --merge along with the liftoff results to get a non-redundant set of transcripts.

[ld9866]

Thanks for your feedback！ I'll then try the method you recommend for testing. Have a good day！