Detects probable locations for single-peak transcription start sites (TSSs) in a sequence. S-Peaker can acquire an UCSC custom track to visualize the probability of observing a single-peak TSS at every position of the sequence. This software is based on a method that identify TSS with the positional sequence features. Transcriptions revealed by strong single peak show that their locations can be mediated by position-specific sequences features.
Permits users to capture 5’ends of RNA polymerase II transcripts. SLIC-CAGE is an unbiased cap-trapper based cap analysis of gene expression (CAGE) protocol allowing users to generate data for genome-wide promoterome. It also enables genome-wide transcription start sites (TSSs) identification from nanogram-scale samples. This application is optimized for promoterome discovery from as little as 5-10 ng of isolated total RNA.
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.
A reproducible clustering pipeline with multiple scales using capped analysis of gene expression (CAGE). RECLU discoveries numerous alternative transcription start sites (TSSs) with the biological implication for your sample.
A straightforward annotation-agnostic computational pipeline that greatly increases confidence in predicted transcription start sites (TSSs) and allows tuning by the end-user to balance both precision and sensitivity of TSS identification to address experimental needs. We provide an analysis of gene coverage and reproducibility, comparisons to previous work, and a software implementation for identification of high confidence TSSs.
You can access more results by creating a free plan account or unlimited content via a premium account.