T3E: a tool for characterising the epigenetic profile of transposable elements using ChIP-seq data.

ABSTRACT:

Background

Despite the advent of Chromatin Immunoprecipitation Sequencing (ChIP-seq) having revolutionised our understanding of the mammalian genome's regulatory landscape, many challenges remain. In particular, because of their repetitive nature, the sequencing reads derived from transposable elements (TEs) pose a real bioinformatics challenge, to the point that standard analysis pipelines typically ignore reads whose genomic origin cannot be unambiguously ascertained.

Results

We show that discarding ambiguously mapping reads may lead to a systematic underestimation of the number of reads associated with young TE families/subfamilies. We also provide evidence suggesting that the strategy of randomly permuting the location of the read mappings (or the TEs) that is often used

SUBMITTER: Almeida da Paz M 

PROVIDER: S-EPMC9710123 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature