Example Fold Analysis
This directory contains a example analysis of Hyb-format and Vienna-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 investigates the predicted folding of miRNA from an experimental replicate infected with Kaposi's Sarcoma-Associated Herpesvirus (KSHV), which are given the type name "KSHV-miRNA". Data from the predicted folding fold for each hybrid record produced by the "Hyb" program are analyzed, and the folds of each KSHV miRNA with a non-miRNA target are characterized to determine the per-base folding folds.
Hybrid sequence information created by the Hyb program and the fold output are provided with the hybkit package in the databases directory, created by downstream analysis of files available at NCBI Gene Expression Omnibus (GEO) GSE101978, at:
The data files can be copied and uncompressed by using the command:
$ sh ./prepare_data.sh
The unpacked data-files require ~150 MB of space. The completed output of the analysis requires ~30 MB of space.
Fold Analysis Example Output
