Transposable element expression software tools | RNA sequencing data analysis
Most RNA-seq data analysis software packages are not designed to handle the complexities involved in properly apportioning short sequencing reads to highly repetitive regions of the genome. These regions are often occupied by transposable elements (TEs), which make up between 20-80% of eukaryotic genomes. They can contribute a substantial portion of transcriptomic and genomic sequence reads, but are typically ignored in most analyses.
Serves for the association of all the meta-data obtained for a given transposable element (TE) family. REPET is a program designed to improve tractability by: (1) interacting with MySQL tables at several key points to take advantage of the SQL language; and (2) handling jobs launched in parallel on a cluster via free batch-queuing systems. This tool is implemented for computationally intensive, or genome-wide analyses.
A method and software package for including both gene- and TE-associated ambiguously mapped reads in differential expression analysis. TEtranscripts shows improved recovery of TE transcripts over other published expression analysis methods, in both synthetic data and qPCR/NanoString-validated published datasets. TEpeaks can be used for analysis of HITS-CLIP data and enhances the method implemented by MACS software by identifying ‘narrow’ peaks.
A computational method to study genome-wide transcriptional regulation of repetitive elements. RepEnrich supports analysis for ChIP-seq and RNA-seq for any organism where a reference genome and repetitive element annotation (such as Repeatmasker annotation) is available. RepEnrich also supports custom repetitive element or repeat feature annotation in bed format.
A coordinated set of pipelines, 'piPipes', to analyze piRNA and transposon-derived RNAs from a variety of high-throughput sequencing libraries, including small RNA, RNA, degradome or 7-methyl guanosine cap analysis of gene expression (CAGE), chromatin immunoprecipitation (ChIP) and genomic DNA-seq. piPipes can also produce figures and tables suitable for publication. By facilitating data analysis, piPipes provides an opportunity to standardize computational methods in the piRNA field.
Provides analysis of TE expression. TEtools takes into account the TE sequence diversity of the genome. It can be applied to unannotated or unassembled genomes and is freely available under the GPL3. This tool performs the mapping of RNA-seq data obtained from classical mRNAs or small RNAs onto a list of TE sequences and performs differential expression analyses with statistical relevance.
Quantifies the contribution of Transposable Elements (TE) promoters to the transcriptome from RNA-seq data. LIONS can annotate the intersection between the assembly, a reference gene set and repeat set. It can be applied to a broad set of data sets for the study of development, stress treatments, aging and cancer. The tool is able to segregate the initiations from non-initiation events.
Reports candidate transposable elements (TEs) to be considered in downstream expression analysis. TEcandidates is a pipeline based on de novo transcriptome assembly. It also includes a modified version of a reference genome suited to map the RNA-seq reads while avoiding ambiguity of the reads coming from TEs. The computer requirements of this program depend on the size of the input RNA-seq, reference genome and TE annotation files to be processed.