SAAP-RRBS pipeline

SAAP-RRBS specifications

Information


Unique identifier OMICS_00612
Name SAAP-RRBS
Alternative name Streamlined Analysis and Annotation Pipeline for RRBS data
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


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Maintainer


  • person_outline Zhifu Sun <>

Publication for Streamlined Analysis and Annotation Pipeline for RRBS data

SAAP-RRBS citation

2015
PMCID: 4790440

[…] dna fragment sequence, which can bias a methylation estimate at these positions. this issue can be addressed by a standalone program trim galore [43] or handled automatically in the later version of saap-rrbs [44]. the tool, bseqc [45], can also be used, which takes aligned sam/bam and generates a new file with the incorporated bases removed., the qc steps for dna illumina microarray […]

SAAP-RRBS institution(s)
Division of Biomedical Statistics and Informatics, Department of Health Sciences Research; Department of Medical Oncology, Mayo Clinic College of Medicine, Chinahester, MN, USA; Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, FL, USA
SAAP-RRBS funding source(s)
Center for Individualized Medicine at Mayo Clinic Rochester, MN, and the 26.2 with Donna Foundation

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