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-chromatin