User manual






Parameters Description
Standard of parameters setting Set related parameters for phasiRNA predictions automatically, including customized, strict, normal and loose.
Phased length Length of phasiRNA cluster, 21nt or 24 nt only
Minimum number of phased position Minimum phased number in phasiRNA cluster
Offset from phased postion Offset value from phased position, 0 or 1 only
P-value The reliability of results, it calculated by improved hypergeometric distribution model
Minimum read count Read count (expression) cutoff value for user-submitted small RNA sequences
Normalization Normalization for user-submitted small RNA sequences, including 0 / Reads per million / Reads per 10 million
Mapping mismatches Mismatches allowed for mapping small RNA sequences to either genomic or transcript datasets
Max multiple mapping Remove multiple mapping that higher than this value




Parameters Description
Phase-initiator source Candidate phase-initiators for identification. User-submitted small RNAs or mature-miRNAs come from miRBase
Distance from start site of phasiRNA cluster to cleavage site Max distance from cleavage site to phasiRNA clusters, (+/-) number * phased length (nt), number between 3 to 7 only
Offset from cleavage site in complimentary region Cleavage site of complimentary region in candidate phase-initiators, 10th (0 offset) or 9~11th (1 offset) only
Other parameters Seed mismatches, Total mismatches and Expectation value.




Parameters Description
Seed mismatches allowed Mismatches happened in seed region (2~13bp)
Total mismatches allowed Mismatches happened in total region
Expectation value for prediction A lower value means more similarity between small RNA and the target mRNA




Parameters Description
Degradome Degradome sequencing data for phasiRNA targets verification
Mismatches allowed for degradomes Mismatches allowed for mapping degradome sequences to transcript (mRNA)
Normalization Normalization for degradome sequencing data, including 0 / Reads per million / Reads per 10 million
Shift allowed Cleavage site of complimentary region of phasiRNAs and target genes, 10th (0 offset) or 9~11th (1 offset) only
t-plot figures Whether present t-plot figures in the result list

Crop Bioinformatics Group, College of Agriculture, NanJing Agricultural University
Contact us at huangji@njau.edu.cn (Ji Huang) or 2016201004@njau.edu.cn (Yuhan Fei)