Example PipelinesΒΆ

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

Each analysis is implemented both using the Python3 API, and as a sequence of shell executable comands 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.



Example Summary 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.