QuickMIRSeq: a pipeline for quick and accurate quantification of both known miRNAs and isomiRs by jointly processing multiple samples from microRNA sequencing.
BACKGROUND
Genome-wide miRNA expression data can be used to study miRNA dysregulation comprehensively. Although many open-source tools for microRNA (miRNA)-seq data analyses are available, challenges remain in accurate miRNA quantification from large-scale miRNA-seq dataset. We implemented a pipeline called QuickMIRSeq for accurate quantification of known miRNAs and miRNA isoforms (isomiRs) from multiple samples simultaneously.


RESULTS
QuickMIRSeq considers the unique nature of miRNAs and combines many important features into its implementation. First, it takes advantage of high redundancy of miRNA reads and introduces joint mapping of multiple samples to reduce computational time. Second, it incorporates the strand information in the alignment step for more accurate quantification. Third, reads potentially arising from background noise are filtered out to improve the reliability of miRNA detection. Fourth, sequences aligned to miRNAs with mismatches are remapped to a reference genome to further reduce false positives. Finally, QuickMIRSeq generates a rich set of QC metrics and publication-ready plots.


CONCLUSIONS
The rich visualization features implemented allow end users to interactively explore the results and gain more insights into miRNA-seq data analyses. The high degree of automation and interactivity in QuickMIRSeq leads to a substantial reduction in the time and effort required for miRNA-seq data analysis.
Early Clinical Development, Pfizer Worldwide Research and Development, Cambridge, MA, 02139, USA. Shanrong.Zhao@pfizer.com.
Shanrong
S
Zhao
Early Clinical Development, Pfizer Worldwide Research and Development, Cambridge, MA, 02139, USA.
William
W
Gordon
Early Clinical Development, Pfizer Worldwide Research and Development, Cambridge, MA, 02139, USA.
Sarah
S
Du
Early Clinical Development, Pfizer Worldwide Research and Development, Cambridge, MA, 02139, USA.
Chi
C
Zhang
Early Clinical Development, Pfizer Worldwide Research and Development, Cambridge, MA, 02139, USA.
Wen
W
He
Early Clinical Development, Pfizer Worldwide Research and Development, Cambridge, MA, 02139, USA.
Li
L
Xi
Business Technology, Pfizer Worldwide Research and Development, Andover, MA, 01810, USA.
Sachin
S
Mathur
Business Technology, Pfizer Worldwide Research and Development, Andover, MA, 01810, USA.
Michael
M
Agostino
Early Clinical Development, Pfizer Worldwide Research and Development, Cambridge, MA, 02139, USA.
Theresa
T
Paradis
Early Clinical Development, Pfizer Worldwide Research and Development, Cambridge, MA, 02139, USA.
David
D
von Schack
I&I Research Unit, Pfizer Worldwide Research and Development, Cambridge, MA, 02139, USA.
Michael
M
Vincent
Early Clinical Development, Pfizer Worldwide Research and Development, Cambridge, MA, 02139, USA. Baohong.Zhang@pfizer.com.
Baohong
B
Zhang
D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D035683:MicroRNAs / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*
D035683:MicroRNAs