Bisulfite treatment is a protocol used in sequencing to detect the methylation state of cytosines in a DNA sequence. It replaces unmethylated cytosines by thymines and, after sequencing and alignment, this reveals the methylation state of a genomic position.
The bisulfite treatment simulator takes paired-end sequencing reads and, using a methylation probability profile, simulates the sample preparation using a treatment of bisulfite. This generates a modified DNA sequence with converted cytosines. The conversion efficiency rates can be adjusted using the parameters λ (unmethylated cytosine conversion rate) and τ (methylated cytosine conversion rate).
- Download the code
git clone https://github.com/bc500/bs_sim.git
- Compile
cd bs_sim
./configure && make
This will generate the binary src/bs_sim.
- Install
The file can be either copied into your user bin directory
cp src/bs_sim ~/bin/
or installed system-wide
sudo make install
Usage:
bs_sim --help
bs_sim --version
bs_sim -i INPUT.BAM -o OUTPUT.BAM [--lambda=<rate>] [--tau=<rate>]
[--methylation-profile=<PROFILE.TBX>]
[--cpg-islands=<CPGIslands.TBX> --methylation-cpg=<rate>]
[--seed=<integer>]
Options:
-h --help Show this screen.
-v --version Show version.
-i --input=FILE Input SAM/BAM file.
-o --output=FILE Output SAM/BAM file.
-l --lambda=<rate> Probability of conversion from cytosine
to thymine [default: 0.99].
-t --tau=<rate> Probability of conversion from methylated cytosine
to thymine [default: 0.05].
-p --methylation-profile=<PROFILE.TBX>
Tabix-format file with methylation probability for
each genomic position.
-c --cpg-islands=<CPGIslands.TBX>
Tabix-format file with CpG Island regions.
-m --methylation-cpg=<rate>
Probability of cytosine being methylated on a CpG Island [default: 0.90].
-s --seed=<integer> Seed for random number generation,
to make experiments repeatable.
./bs_sim -i sample.bam -o sample_bs.bam -p methylation.tbx -c CpGs.tbx
./bs_sim -i sample.bam -o sample_bs.bam -p methylation.tbx -c CpGs.tbx -l 0.98 -t 0.03 -m 0.8