Software and supporting material for "SMAP: a streamlined methylation pipelinefor bisulphite sequencing".
Dataset type: Software, Workflow, Epigenomic
Data released on June 30, 2015
DNA methylation plays important roles in regulating gene expression and cellular specification. Reduced representation bisulfite sequencing (RRBS) has become prevailing in methylation studies due to its cost-effectiveness and single-base resolution. The rapid accumulation of RRBS data demands ingeniously and practically designed analytical tools. To streamline the data processing of DNA methylation in multiple RRBS samples, we present a flexible pipeline named SMAP, whose features include: 1) it handles single- and/or paired-end (SE/PE) diverse bisulfite sequencing data with reduced false positive rate in differentially methylated regions; 2) it detects allele-specific methylation events with improved algorithm; 3) it has a build-in pipeline for novel single nucleotide polymorphisms (SNP) detection; 4) it supports user-defined multiple restriction enzymes; 5) it basically conducts a one-step operation in all methylation analyses. SMAP is a modular pipeline implemented in Perl that calls software components written in C/C++, Perl, R and Java. Required input files for SMAP include BS or RRBS data in FASTQ format and a user-defined configuration file including all settings of the pipeline
Keywords:
Additional details
Read the peer-reviewed publication(s):
(PubMed: 26140213)
Additional information:
https://github.com/gaosjlucky/SMAPdigger
Accessions (data generated as part of this study):
SRA:
SRA269060
Sample ID | Taxonomic ID | Common Name | Genbank Name | Scientific Name | Sample Attributes |
---|---|---|---|---|---|
K1_MB | 9606 | Human | human | Homo sapiens | Patient:K1 Tissue:brain(UBERON:0000955) Is tumor:yes ... + |
K1_MVC | 9606 | Human | human | Homo sapiens | Patient:K1 Tissue:blood vessel(UBERON:0001981) Is tumor:yes ... + |
K1_normal | 9606 | Human | human | Homo sapiens | Patient:K1 Tissue:Kidney(UBERON:0002113) Is tumor:no ... + |
K1_pRCC | 9606 | Human | human | Homo sapiens | Patient:K1 Tissue:Kidney(UBERON:0002113) Is tumor:yes ... + |