RRBS Analyser for DNA methylation analysis

Upload FASTQ file

Cloud storage is simply a term that refers to online space that you can use to store your data. It provides a convenient way of remotely storing your important data. Cloud storage can provide the benefits of greater accessibility and reliability, rapid deployment, and archival and disaster recovery purposes.Cloud storage solutions are usually provided using a large network of virtual servers that also come with tools for managing files and organizing your virtual storage space.This infrastructure is installed and managed by highly specialized providers. Box (https://www.box.com) is a cloud storage service that allows individuals to upload and access files from any device with an Internet connection quickly and easily. Box can be used to share files and collaborate with any individual with an email address. BOX is also a pioneer in robust content-management security. BOX is used as one of ways for RRBS-analyser data uploading. As the Internet is constantly changing, a public interface that are more suitable to cloud-based systems may emergent in the future, RRBS-server will update the interface for the users.

In this page, only one sample is allowed for quality assessments of sequencing data, methylation sites annotation. Both single end and paired end sequencing data allowed. Firstly upload files to box, then input.

>> Step 1: Upload FASTQ files to FTP address or box, the source data are required in specified input file format (*.fq.tar.bz2 or *.fq.tar.gz or *.fq.tar or *.fq.gz). Upload file with a restricted file size of maximum 2G.

>> Step 2: Follow the prompts to input file names.

>> Step 3: Users can choose reference genome through scroll bars to choose specific category and species for sequence reads alignment.

>> For default test data, above three steps could be ignored!

>> Format introduction of FASTQ file: you can find detail format information in " Input file introduction" page.

Upload SAM files

In this page, one sample or multiple samples is allowed, single sample only for methylation sites annotation, multiple samples for methylation sites annotation, differentially methylated regions identification. For multiple samples, touch the "Add more" button and then upload each sample files separately.

>> Step 1: Upload SAM files to FTP address or box, the source data are required in specified input file format (*.sam.tar.bz2 or *.sam.tar.gz or *.sam.tar or *.sam.gz). Upload file with a restricted file size of maximum 2G.

>> Step 2: Follow the prompts to input file names.

>> Step 3: Users can choose reference genome through scroll bars to choose specific category and species for sequence reads alignment.

>> For default test data, above three steps could be ignored!

>> Step 2: Users can choose reference genome through scroll bars to choose specific category and species for annotation file selection.

>> Format introduction of SAM file: you can find detail format information in " Input file introduction" page.

Upload MC files

In this page, one sample or multiple samples is allowed, single sample only for methylation sites annotation, multiple samples for methylation sites annotation, differentially methylated regions identification. For multiple samples, touch the "Add more" button and then upload each sample files separately.

>> Step 1: Upload MC files to FTP address or box, the source data are required in specified input file format (*.mc.tar.bz2 or *.mc.tar.gz or *.mc.tar or *.mc.gz). Upload file with a restricted file size of maximum 20M each sample.

>> Step 2: Follow the prompts to input file names.

>> Step 3: Users can choose reference genome through scroll bars to choose specific category and species for sequence reads alignment.

>> For default test data, above three steps could be ignored!

>> Format introduction of MC file: you can find detail format information in " Input file introduction" page.

Select parameters for FASTQ/ SAM/MC files

>> Quality assessment for FASTQ file

For the sequencing quality analysis of FASTQ raw data, there are several parameters that users can set for assessment, such as sequencing quality value, quality score to filter, shortest length of the remaining reads, error rate threshold for filter, enzyme type, adapters for filter.

>> Bisulfite treated reads alignment for FASTQ file

For the sequencing alignment analysis of FASTQ raw data, there are several parameters that users can set for alignment, such as maximum number of mismatches allowed on a read, maximum number of equal best hits to count, restriction enzyme digestion sites, maximum number of N in read for filter, mapping protocol.

>> DNA methylation analysis for FASTQ SAM or MC file

For the whole genome methylation analysis of FASTQ or SAM or MC file, there are several parameters that users can set for analysis, such as sequencing depth filter(n value),element which (element region overlapped captured reads)bp/(element region)bp > P will be selected for methylation analysis in a map(p value) , Methylation scales(l1,l2,l3,l4).
PE value is useful only for SAM file(if users select "no", which means the uploaded SAM format data generated by single end sequencing technology, otherwise paired end sequencing technology.).

>> DMR analysis for multiple SAM or MC files

For the differently methylated regions analysis of multiple SAM or MC files, there are several parameters that users can set for analysis, such as lowest coverage of cytosine reads to use, methods of detect DMRs, cytosine type for detection, lowest coverage of cytosine reads to use, lowest number of selected type of cytosine in the window, step size of the sliding processes, max/min methylation level difference, value of max-min methylation level, lowest length to join two fragments into one, p value to judge as a DMR, fdr to adjust DMR p value, left flanking region length of DMR in a map, right flanking region length of DMR in a map .

E-mail notification

Users can enter their email address or not, through which automatically job ID number can be delivered to customer for further result retrieve.
This server takes a brief time (up to several hours) to perform the analysis.
The server will automatically send a notification mail with the result link to users, if email address has been filled.

User Page

Quick-start guide manual

Index

Overview

What can RRBS-Analyser do for you?

How to use RRBS-Analyser server?

Workflow scheme

Explanation of inputs

Upload FASTQ file

Upload SAM files

Upload MC files

Select parameters for FASTQ/ SAM/MC files

E-mail notification

Feedback

About us

Links

Analysis/Upload

Reanalysis

Results

Test data for RRBSAnalyser:

SAM/MC results

FASTQ results

Annotation