Frequently Asked Questions

What type of data can be processed by icSHAPE-pipe?

Initially, icSHAPE-pipe was primarily designed to process RNA secondary structure sequencing data of the icSHAPE type. The main idea is to map the sequencing data to the genome and use the sliding window method to calculate the reactivity score of each base. This calculation method can improve the problem that the reads map to transcript are diluted in previous pipeline, and the sliding window method also makes The calculated value is more accurate.

We can also apply icSHAPE-pipe to other types of structural sequencing data, such as PARS. Since DMS-Seq only considers A/C bases, this feature has been added in versions 2.0.0 and later.In the future, we will also consider adding functions to process data such as SHAPE-Map.

What quality control can icSHAPE-pipe do?

icSHAPE-pipe has the following additional features:

• Calculate RT correlation between replicates
• Count the number of RTs per base
• Count the proportion of remaining reads processed at each step
• Statistical distribution of activity score
• Genomic reactivity conversion to transcript reactivity
• Reactivity statistics for different gene types
• Evaluate score with known structure