Reanalysis

Reanalysis file format

Upload data
Sample upload:
job ID:
Example job ID:1394150952
reference genome:

Email
Email input:  emailoptional
Password for RRBSAnalyser@163.com: bioinfo@2011jyz

Parameters
Identified 5mC sites
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u value: process only unique mappings, default:no
m value: report loci with sequencing depth>= m FOLD, default:1
p value: process only properly paired mappings, default:no (only for paired end)
z value: report loci with zero methylation ratios, default:yes
If you choose the following parameters, default values will be used in the above four parameters !
DNA methylation analysis
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PE value: Paired end alignment data, default:no
n value: FOLD, analysis loci with sequencing depth>=n FOLD, default:5
P value: element which (element region overlapped captured reads)bp/(element region)bp > P will be       selected for methylation analysis in a map, default:0(0-1]
Methylation scales[1-99]:
l1 value: methylation level for first scale in a map, default:20(%)
l2 value: methylation level for second scale in a map, default:40(%)
l3 value: methylation level for third scale in a map, default:60(%)
l4 value: methylation level for fourth scale in a map, default:80(%)
DMR analysis parameters are valid only for multiple samples.
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c value: lowest coverage of cytosine reads to use, default:4
m value: choose one method to detect DMRs, only ANOVA or Kruskal for three or more samples' DMR detection; two samples, default: ChiSquare
CT value: cytosine type < C|CG||CHG||CHH >, default:"CG"
LW value: length of a sliding window to identified DMRs, default:200(bp)
NC value: lowest number of selected type of cytosine in the window, default:5
SL value: step size of the sliding processes, default:10(bp)
MR value: max/min methylation level difference, default:1.5
DM value: value of max-min methylation level, default:0.1
LD value: lowest length to join two fragments into one, default:100(bp)
p value: p value to judge as a DMR, default:0.01
fdr value: fdr to adjust DMR p value, default:0.05
LL value: left flanking region length of DMR in a map, default:1000(bp)
RL value: right flanking region length of DMR in a map, default:1000(bp)