mirTools 2.0 - for non-coding RNA discovery, profiling and functional annotation based on high-throughput sequencing

            for non-coding RNA discovery, profiling and functional annotation based on high-throughput sequencing
Two case Analysis | mirTools 2.0 - for non-coding RNA discovery, profiling and functional annotation based on high-throughput sequencing
Start analysis
 
 Two Case Analysis
Sequences upload
Reference genome selection
   Reference Genome:
Samples upload: Raw sequences (*.fa or *.gz or *.zip, Max 30M) Mapping results (*.bam, Max 30M)
   Sample Data A: Example sampleA   
   Sample Data B: Example sampleB
   Length of interval: --
Your email:   (Optional) Example output
ncRNA annotation and profiling
Parameters for SOAP to align reference genome:
   M value: Match mode: 0=exact; 1=1 mismatch; 2=2 mismatch; 3=all; 4=the best
   R value: How to report repeat hits: 0=none; 1=random one; 2=all
   V value: Maximum number of mismatches
Parameters for MEGABLAST to align miRBase and Rfam:
   E value: Expect value
   B value: Number of database sequence to show alignments for (B)
   V value: Number of database sequences to show one-line descriptions for (V)
Filter for miRNA isoform:
   Absolute reads count >:
   Contributes to the total number (%):
   Use Z-score cut-off :
Parameters for novel miRNA prediction
  miReap miRDeep
Parameters for novel microRNAs prediction tools
 miReap
   L value: Flank sequence length of the query. Range 0 - 200
 miRDeep
   V value: The score cut-off which reflects the probability that the hairpin is a genuine miRNA precursor
 
miRNA targets prediction and functional annotation
Parameters for miRNA targets prediction:
Select the top abundant miRNA for targets prediction
   Known miRNA:
   Novel miRNA:
Select main tools for targets prediction
   miRanda RNAhybrid
Parameters for miRNA targets prediction tools
 miRanda
   Energy: Minimal free energy (MFE)
   Score:
 RNAhybrid
   Energy: Minimal free energy (MFE)
   P value:
Select additional tools for miRNA for targets prediction.
   MicroCosm microT_v3.0 MirTarget2
    miRNAMap TargetScan TargetSpy
Parameters for GO and Pathway analysis of miRNA targets:
Parameters for GO analysis
   P value: The threshold for hypergeometric test
   Enrichment fold:
Parameters for Pathway analysis
   P value: The threshold for hypergeometric test
   Enrichment fold:
Parameter for protein-protein interaction analysis of miRNA targets:
   Score:
 
Differential expression analysis
Parameters for detecting differentially expressed miRNAs:
   P value: P value inferred based on Bayesian method
   D value: Fold change in normalized sequence counts
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Institute of Genomic Medicine, Wenzhou Medical College
Wenzhou 325035, Zhejiang, China