Example Analyses

This section includes multiple example stepwise analyses of data from a qCLASH experiment described in [Gay2018], with data acquired from the NCBI Gene Expression Omnibus (GEO) accession GSE101978.

Each analysis is implemented both using the Python3 API, and as a sequence of shell executable commands in a bash script. The Python API implementations are generally significantly more efficient as more steps can be performed on a single iteration over the input data.

Each analysis performs quality control steps on the data by checking data integrity (hyb_check) and removing artifactual ribosomal- and mitochondrial-RNA hybrids (hyb_filter). Further filtration may be performed, and then each described analysis is carried out.

Pipeline	Description
Example Type-miRNA Analysis	Quantify the sequence and miRNA types in a hyb file
Example Target Analysis	Analyze targets of a set of miRNAs from a single experiment
Example Grouped Target Analysis	Analyze and plot targets of a set of miRNAs from pooled experimental replicates
Example Fold Analysis	Analyze and plot predicted miRNA folding patterns in miRNA-containing hybrids

Further details on each respective example analysis can be found in each section.

• Example Type-miRNA Analysis
  • Type-miRNA Analysis Example Output
• Example Target Analysis
  • Target Analysis Example Output
• Example Grouped Target Analysis
  • Grouped Target Analysis Example Output
• Example Fold Analysis
  • Fold Analysis Example Output