Oct 29, 2024 · CAGEr package supports three types of CAGE data input: Sequenced CAGE tags mapped to the genome: either BAM (Binary Sequence Alignment Map) files of sequenced CAGE tags aligned to the referent genome (including the paired-end data such as CAGEscan) or BED files of CAGE tags (fragments).

Nov 1, 2024 · Cap Analysis of Gene Expression (CAGE) is one of the most popular 5’-end sequencing methods. In a single experiment, CAGE can be used to locate and quantify the expression of both Transcription Start Sites (TSSs) and enhancers.

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Jan 17, 2021 · CAGE [@Kodzius:2006] is a high-throughput method for transcriptome analysis that utilizes cap trapping [@Carninci:1996], a technique based on the biotinylation of the 7-methylguanosine cap of Pol II transcripts, to pulldown the 5′-complete cDNAs reversely transcribed from the captured transcripts.

Oct 29, 2024 · There are several large collections of CAGE data available that provide single base-pair resolution TSSs for numerous human and mouse primary cells, cell lines and tissues.

Preprocessing of CAGE sequencing data, identification and normalization of transcription start sites and downstream analysis of transcription start sites clusters (promoters).

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Jan 17, 2021 · Preprocessing of CAGE sequencing data, identification and normalization of transcription start sites and downstream analysis of transcription start sites clusters (promoters).

Feb 4, 2015 · Here we present CAGEr, an R implementation of novel methods for the analysis of differential TSS usage and promoter dynamics, integrated with CAGE data processing and promoterome mining into a first comprehensive CAGE toolbox on a common analysis platform.

Jan 17, 2021 · The CAGEr package performs identification of transcription start sites and frequency of their usage from input CAGE sequencing data, normalization of raw CAGE tag count, clustering of TSSs into tag clusters (TC) and their aggregation across multiple CAGE experiments to construct the promoterome.