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Data released on June 30, 2015

Software and supporting material for "SMAP: a streamlined methylation pipelinefor bisulphite sequencing".

Chen, G; Gao, S; Huang, Y; Jia, W; Li, D; Mao, L; Wu, S; Zhao, S; Zhou, Q; Zou, D; Chen, H; Chen, M; Xia, F; Bolund, L; Orntoft, T, F; Sorensen, K, D (2015): Software and supporting material for "SMAP: a streamlined methylation pipelinefor bisulphite sequencing". GigaScience Database. http://dx.doi.org/10.5524/100143 RIS BibTeX Text

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

Contact Submitter

Related manuscripts:

doi:10.1186/s13742-015-0070-9

Additional information:

https://github.com/gaosjlucky/SMAPdigger

Accessions (data included in GigaDB):

SRA: SRA269060

Keywords:

Reduced representation bisulfite sequencing (RRBS) differentially methylated regions (DMR) allele-specific DNA methylation (ASM) 

Epigenomic, Workflow, Software

http://gigadb.org/images/data/cropped/100143_SMAP_workflow.jpg

Funding:

  • Funding body - Danish Strategic Research Council
  • Funding body - The Danish Cancer Society
  • Funding body - National Natural Science Foundation of China
  • Award ID - 61202127
  • Funding body - Ministry of Education of the People's Republic of China
  • Award ID - 60911062

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
K1_MB9606HumanhumanHomo sapiens Patient ID:K1
Tissue type:brain(UBERON:0000955)
Is tumor:yes
...
+
K1_MVC9606HumanhumanHomo sapiens Patient ID:K1
Tissue type:blood vessel(UBERON:0001981)
Is tumor:yes
...
+
K1_normal9606HumanhumanHomo sapiens Patient ID:K1
Tissue type:Kidney(UBERON:0002113)
Is tumor:no
...
+
K1_pRCC9606HumanhumanHomo sapiens Patient ID:K1
Tissue type:Kidney(UBERON:0002113)
Is tumor:yes
...
+
Displaying 1-4 of 4 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile TypeFile FormatSizeRelease Date 
K1_normalMethylome dataFASTQ1.84 GB2015-05-20
K1_normalMethylome dataFASTQ1.6 GB2015-05-20
K1_normalMethylome dataFASTQ1.73 GB2015-05-20
K1_normalMethylome dataFASTQ1.47 GB2015-05-20
K1_MBMethylome dataFASTQ1.73 GB2015-05-20
K1_MBMethylome dataFASTQ1.52 GB2015-05-20
K1_MBMethylome dataFASTQ1.57 GB2015-05-20
K1_MBMethylome dataFASTQ1.33 GB2015-05-20
K1_pRCCMethylome dataFASTQ1.03 GB2015-05-20
K1_pRCCMethylome dataFASTQ874.29 MB2015-05-20
Displaying 1-10 of 57 File(s).

History:

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