Reanalysis

Reanalysis file format

Upload data
Sample upload:
job ID:
Example job ID:1396078490
reference genome:
 

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

Parameters
Quality assessment
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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:20
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:50bp
error rate: maximum allowed error rate (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, defaul:none
adapter B: only for paired end, defaul:none
Bisulfite treated reads alignment
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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:5
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
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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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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(%)