This is the Linux app named MspJI-seq_pipeline1.0 whose latest release can be downloaded as pipeline1.0.tar.gz. It can be run online in the free hosting provider OnWorks for workstations.
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MspJI-seq_pipeline1.0
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DESCRIPTION
MspJI-seq_pipeline1.0 is pipeline for MspJI-digesting sequencing in DNA methylation study. Modification-dependent restriction endonuclease MspJI digestion coupled with next generation sequencing could estimate the methylation state of "CNNR" Cytosine location in the genome by mapping high throughput reads to the reference sequences. MspJI-seq_pipeline1.0 is designed to be a general-purpose mapping program to handle these special characteristics of MspJI-seq. Its alignment is based on the open source program SOAP (Short Oligo Alignment Program), and mCNNR sites recognition is performed by regular expression in perl.
Audience
Science/Research
Programming Language
Perl
Database Environment
Flat-file
Categories
This is an application that can also be fetched from https://sourceforge.net/projects/mspjiseqpipelin/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.
