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We designed and implemented a pipeline called QAmiRSeq for fast and accurate quantification of both known miRNAs and isomiRs from high throughput sequencing. QAmiRSeq reconciles its implementation with the unique nature of miRNAs. It is the first algorithm that takes advantage of the strand information for more accurate quantification. All analyses results are organized in a user friendly manner, accessible via a web interface, and can be drilled down interactively by investigators or analysts to conduct further investigation and discovery. QAmiRSeq is a powerful and flexible open source tool for accurate quantification of known miRNAs/isomiRs from both small and large number of samples.
The software package, and the test run results for miRNA-seq dataset GSE64977(human), GSE65920(mouse) and GSE60900(rat) can be downloaded directly from https://sourceforge.net/projects/qamirseq/files/, and are also available online https://baohongz.github.io/QAmiRSeq/
Features
- Strand aware
- Quantification of both miRNAs and isomiRs
- Joint mapping of multiple samples
- Accurancy and reliablity of detected miRNAs
- Comprehensive annotation and and rich running metrics for data QC
- Flexibility in counting reads with mismatches
- User friendly summary report
Project Samples
