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BSMAP specifications


Unique identifier OMICS_00579
Alternative name Bisulfite Sequence Mapping Program
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTQ, BAM
Output format SAM/BAM, BSP, text
Operating system Unix/Linux
Programming languages C++
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes


No version available



  • person_outline Wei Li

Publication for Bisulfite Sequence Mapping Program

BSMAP citations


Genome wide determination of on target and off target characteristics for RNA guided DNA methylation by dCas9 methyltransferases

PMCID: 5888497
PMID: 29635374
DOI: 10.1093/gigascience/giy011

[…] ow-quality reads, 953.7 Gb 150 bp paired-end clean data were generated. An average of 106 Gb clean data were obtained for each sample. Clean reads were aligned to the human reference genome (hg19) by BSMAP (v2.74) with the parameter “-u -v 5 -z 33 -p 6 -n 0 -w 20 -s 16 -r 0 -f 10 -L 140” []. Only the CpG sites with read depths ≥4 were taken into consideration for DNA methylation level calculation. […]


Parental micronutrient deficiency distorts liver DNA methylation and expression of lipid genes associated with a fatty liver like phenotype in offspring

Sci Rep
PMCID: 5812986
PMID: 29445184
DOI: 10.1038/s41598-018-21211-5
call_split See protocol

[…] ing from bisulfite converted libraries were trimmed of adapter sequences and low quality regions using Trimmomatic (version 0.32) and mapped to the genome (GRCz10, Ensembl zebrafish genome) using the BSMAP program. The resulting bam files were then sorted and indexed using SAMtools (Ver. 1.2.) and the methylation levels extracted as bed files, bisulfite conversion rates and CpG motif counts using […]


Targeted DNA demethylation of the Arabidopsis genome using the human TET1 catalytic domain

Proc Natl Acad Sci U S A
PMCID: 5834696
PMID: 29444862
DOI: 10.1073/pnas.1716945115

[…] DNA was extracted using a CTAB-based method and 100 ng were used to make libraries using the Nugen Ultralow Methyl-seq kit (Ovation). Raw sequencing reads were aligned to the TAIR10 genome using BSMAP () by allowing up to two mismatches and only retaining reads that mapped to one location. Methylation ratios are calculated by #C/(#C+#T) for all CG, CHG, and CHH sites. Reads with three consecu […]


Genome wide tracking of dCas9 methyltransferase footprints

Nat Commun
PMCID: 5807365
PMID: 29426832
DOI: 10.1038/s41467-017-02708-5
call_split See protocol

[…] re purified with a 1× Agencourt RNA XP bead cleanup and sequenced on the HiSeq 2500 or NextSeq 500 Sequencing System (Illumina). Sequenced reads were aligned to the mm9 or hg19 reference genome using BSmap. Custom scripts were used to determine whether cytosines were methylated or unmethylated by observing bisulfite conversion of unmethylated cytosines in comparison to the reference sequence. […]


Genome wide analyses reveal a role of Polycomb in promoting hypomethylation of DNA methylation valleys

Genome Biol
PMCID: 5806489
PMID: 29422066
DOI: 10.1186/s13059-018-1390-8

[…] For WT and mutant mESCs, MethylC-seq reads were aligned to mm9 using the Bisulfite Sequence Mapping Program (BSMAP) [] with parameters –r 0 –w 100 –v 0.1 –A AGATCGGAAGAGC. Multi-mapped reads and PCR duplicates were removed. After mapping, those 200-bp bins with total CG co […]


Genome wide DNA methylation analysis reveals that mouse chemical iPSCs have closer epigenetic features to mESCs than OSKM integrated iPSCs

PMCID: 5833453
PMID: 29416007
DOI: 10.1038/s41419-017-0234-x

[…] l followed by bisulfite conversion. Libraries were sequenced on an Illumina HiSeq 2500 sequencer as paired-end 50-bp reads.Sequencing reads of RRBS were aligned to mouse reference genome (mm10) using BSMAP v2.90 with up to 8% mismatches. Only uniquely mapped pairs were retained for analysis of DNA methylation. MOABS v1.3.2 was used to merge replicates and measure CpG methylation levels. Only the C […]


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BSMAP institution(s)
Division of Biostatistics, Dan L Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA

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