CAGE-seq clusters

Cluster count table from frontal CAGE-seq data of RiMod-FTD resource (https://www.rimod-ftd.org/).

The data was processed as follows:

Sequencing adapters and barcodes in CAGE-seq FastQ files were trimmed using Skewer (v.0.1.126). Sequencing artefacts were removed using TagDust (v1.0)1 Processed reads were then aligned against the human genome hg38 using STAR (v.2.4.1). On average, 16,306,077 could be uniquely mapped per sample (76% uniquely mapped on average reads per sample). CAGE detected TSS (CTSS) files were created using CAGEr (v1.10.0). With CAGEr, we removed the first G nucleotide if it was a mismatch. CTSS were clustered using the ‘distclu’ method with a maximum distance of 20 bp. For exact commands used we refer to the reader to the scripts used in this pipeline: https://github.com/dznetubingen/cageseq-pipeline-mf. In total, we could identify 47,298 different peaks. Data was normalized to counts per million (CPM) for visualization on the website.