Installation

Software requirements

  • Python 3.x.x

  • BEDTools

  • gffread

Obtain TEIRI

git clone https://github.com/janky-yz/TEIRI.git

Inputs you should prepare

  • GTF files from short-read RNA-seq transcript assembly (for example, from StringTie)

  • BED12 file generated by flair correct from long-read RNA-seq

  • TSS signal table in TSV format (CAGE and/or RAMPAGE support)

  • TE annotation BED file

  • eRNA annotation BED file

  • Reference annotation GTF