Installation

Software requirements

• Python 3.12.3

• BEDTools

• gffread

• numpy

• pandas

• torch

• selene_sdk

• pyBigWig

• scipy

• matplotlib

• tabix

Obtain Deep-TEIRI

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

Inputs you should prepare

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

• Two CPM-normalized bigWig files (uniquely mapped reads and multi-mapped reads)

• TE annotation BED file

• Reference annotation GTF file

• Reference FASTA file

• Chromosome length file