Data submission

Function and data introduction

The web server RRBS-Analyser is developed for comprehensive characterizing the methylome in one or multiple samples. It is intended to identify and annotate the methylation sites and inspect the differentially methylated regions.
Only FASTQ, SAM or MC format files are allowed in RRBS-Analyser.The introductions are depicted in "Input file introduction". If you choose FASTQ format file to upload, only one sample is allowed, for SAM and MC formats, both simple and multiple samples are allowed.

Input format

Upload data
Firstly: using ftp tools to upload file.
If so, please select ftp; Username: rrbsanalyser   Password: rb18fa6dan!    
IP:122.228.158.106         port: 2121
Or click here or https://www.box.com/ to upload file to box
  Username: RRBSAnalyserTest@gmail.com   Password: RRBSA2011
Secondly: After upload successfully, input your file names, for multiple samples, each file name separated by comma (,)
                        such as Sample1.sam.tar.gz,Sample2.sam.tar.gz
If users want test RRBS-Analyser with default data, only need to touch the "submit" button.
   Example1   SAM:  
   Example2         Example3   (*.sam or *.sam.tar.bz2 or *.sam.tar.gz or *.sam.gz or *.sam.tar, Max 6 samples )
reference genome:

Email
Email input:  emailoptional
Password for RRBSAnalyser@163.com: bioinfo@2011jyz
Due to the data set needed to analysis is too large, please wait patiently.

Parameters
Identified 5mC sites
    Hide Parameters
u value: process only unique mappings, default:no
m value: report loci with sequencing depth>= m FOLD, default:1
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
    Hide Parameters
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.
DMR analysis
    Hide Parameters
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:5(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)