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 paired end sequencing data, each file name separated by comma (,)
                        such as Sample1_1.fq.tar.gz,Sample1_2.fq.tar.gz
If users want test RRBS-Analyser with default data, only need to touch the "submit" button.
 Example_1  fq:  
    (*.fq or *.fq.tar.bz2 or *.fq.tar.gz or *.fq.tar or *.fq.gz )
reference genome:

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

Parameters
Quality assessment
    Hide Parameters
phred: base quality, Illumina is using 64, Sanger Institute is using 33, default:33
qual: the cut-off value for PHRED quality score for high-quality filtering, default:16
length: discard reads that became shorter than length INT because of either quality or adapter       trimming. A value of '0' effectively disables this behaviour, default:15bp
error rate: maximum allowed error rate during filter adapter (no. of errors divided by the length of the matching region),       default: 0.1
enzyme: Specifies that the input file was an MspI digested,[y/n]; default=yes
adapter A: single end, default:none
adapter B: only for paired end, default:none
Bisulfite treated reads alignment
    Hide Parameters
s value: seed size, min=8, max=16,For RRBS mode, seed length is fixed to 12
v value: maximum number of mismatches allowed on a read, <=15. default:2
w value: maximum number of equal best hits to count, smaller will be faster, <=1000, default:100
d value: restriction enzyme digestion sites, digestion position marked by '-', default:C-CGG for MspI
r value: how to report repeat hits, 0=none(unique hit/pair only); 1=random one, default:1
f value: filter low-quality reads containing >n Ns, default:5
p value: setting mapping strand information, [0/1], default:0; 0: only map to 2 forward strands, i.e.       BSW(++) and BSC(-+),for PE sequencing, map read#1 to ++ and -+, read#2 to +- and --. 1:       map SE or PE reads to all 4 strands, i.e. ++, +-, -+, --
Im: only for paired end, minimal insert size allowed, default:20 bp
Ix: only for paired end, maximal insert size allowed, default:400 bp
Identified 5mC sites
    Hide Parameters
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
    Hide Parameters
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(%)