This is the Linux app named MethylExtract to run in Linux online whose latest release can be downloaded as MethylExtract.tgz. It can be run online in the free hosting provider OnWorks for workstations.
Download and run online this app named MethylExtract to run in Linux online with OnWorks for free.
Follow these instructions in order to run this app:
- 1. Downloaded this application in your PC.
- 2. Enter in our file manager https://www.onworks.net/myfiles.php?username=XXXXX with the username that you want.
- 3. Upload this application in such filemanager.
- 4. Start the OnWorks Linux online or Windows online emulator or MACOS online emulator from this website.
- 5. From the OnWorks Linux OS you have just started, goto our file manager https://www.onworks.net/myfiles.php?username=XXXXX with the username that you want.
- 6. Download the application, install it and run it.
MethylExtract to run in Linux online
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DESCRIPTION
MethylExtract is a user friendly tool to generate i) high quality, whole genome methylation maps and ii) to detect sequence variation within the same sample preparation. The program is implemented into a single script and takes into account all major error sources: sequencing errors, bisulfite failure, clonal reads and single nucleotide variants. MethylExtract detects variation (SNVs – Single Nucleotide Variation) in a similar way than VarScan, a very sensitive method extensively used in SNP and genotype calling based on non-bisulfite treated reads.Features
- Methylation and SNV calling from NGS BS-Seq experiments
- Detects and removes potential PCR duplicates
- Putative bisulfite failures detection
- Sequencing errors control
- Statistical bisulfite failure assessment
- Bisulfite SAM / BAM files processing
- Multithreading and memory control
Programming Language
Perl
This is an application that can also be fetched from https://sourceforge.net/projects/methylextract/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.
