QC for Targeted Sequencing

This tool is designed to report the performance (enrichment and specificity) of a targeted re-sequencing experiment. Targeted re-sequencing is due to its low costs, very popular and several companies provide platforms and protocols (learn more at http://en.wikipedia.org/wiki/Exome_sequencing#Target-enrichment_strategies). Array-based approaches are offered by e.g. Agilent (SureSelect) and Roche Nimblegen. Furthermore, amplicon sequencing with PCR primers is offered by RainDance, Fluidigm and others.

Given an annotation track with the target regions (e.g. imported from a bed file), this tool will investigate a read mapping to determine whether the targeted regions have been appropriately covered by sequencing reads as well as information about how specific the reads map to the targeted regions. The results are provided both as a summary report and as track or table with detailed information about each targeted region.

Note! This tool is for re-sequencing data only; if you have RNA-seq data, please see RNA-Seq Analysis.


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