github.com/broadinstitute/broad-epi-repeats-analysis/Align-quantify-repeats

Transposable Elements Pipeline Analysis

Introduction

This repository contains a collection of pipelines and scripts to analyze RNA-seq and ChIP-seq data taking into account multi-mapping reads for accurate transposable elements quantification.

RNA

TEtranscript toolkit is used for multi-mappers-awar family-level quantifications and for differential analyses.

TElocal is used for m


This is a companion discussion topic for the original entry at github.com/broadinstitute/broad-epi-repeats-analysis/Align-quantify-repeats