Example Type-miRNA Analysis
This directory contains a example analysis of Hyb-format data, published in the quick Crosslinking and Sequencing of Hybrids (qCLASH) experiment described in: Gay, Lauren A., et al. "Modified cross-linking, ligation, and sequencing of hybrids (qCLASH) identifies Kaposi's Sarcoma-associated herpesvirus microRNA targets in endothelial cells." Journal of virology 92.8 (2018): e02138-17.
- The analysis is carried out in multiple example implementations which produce identical output:
via the Command-Line
via the Python3 API
This analysis first performs quality control on the data. It then summarizes and analyzes the hybrid, segment, and miRNA characteristics of each input file. Analyses for each individual file, and a combined summary analysis are all produced.
The sequencing information is available at NCBI Gene Expression Omnibus (GEO) GSE101978, at:
The data files can be downloaded and uncompressed by using the command:
$ sh ./download_data.sh
The unpacked hyb data-files require ~2 GB of space. The completed output of the analysis requires ~1.5 GB of space.
Type-miRNA Analysis Example Output
