TY  - JOUR
A1  - Karunanithi, Sivarajan
A1  - Simon, Martin
A1  - Schulz, Marcel Holger
T1  - Automated analysis of small RNA datasets with RAPID
T2  - PeerJ
N2  - Understanding the role of short-interfering RNA (siRNA) in diverse biological processes is of current interest and often approached through small RNA sequencing. However, analysis of these datasets is difficult due to the complexity of biological RNA processing pathways, which differ between species. Several properties like strand specificity, length distribution, and distribution of soft-clipped bases are few parameters known to guide researchers in understanding the role of siRNAs. We present RAPID, a generic eukaryotic siRNA analysis pipeline, which captures information inherent in the datasets and automatically produces numerous visualizations as user-friendly HTML reports, covering multiple categories required for siRNA analysis. RAPID also facilitates an automated comparison of multiple datasets, with one of the normalization techniques dedicated for siRNA knockdown analysis, and integrates differential expression analysis using DESeq2.
KW  - Comparative analysis
KW  - sRNA tool
KW  - Automated sRNA analysis
KW  - sRNA
KW  - Small RNA analysis
KW  - Computational sRNA analysis
KW  - siRNA analysis
KW  - siRNA quantification
KW  - Eukaryotic sRNA
Y1  - 2019
UR  - http://publikationen.ub.uni-frankfurt.de/frontdoor/index/index/docId/73717
UR  - https://nbn-resolving.org/urn:nbn:de:hebis:30:3-737175
SN  - 2167-8359
VL  - 7
IS  - e6710
PB  - PeerJ, Inc.
CY  - London [u.a.]
ER  -