MethylPurify 2.0-20141116

Get Dependent data

Get the version of genome fasta that you mapped your fastqs, we support hg18 and hg19 genome fasta now, take hg19 as an example

## use built-in script
cd methylpurify/db
bash genome.sh hg19

Get Dependent software

• samtools, version 0.2.0

• numpy, version 1.8.2

• pyfasta, version 0.5.2

Easy to start

Input: BAM file, this should be mapped with BSMap with -R option * BSMap

Currently, we only support hg19 and hg18 genome index mapped BAM file.

If your fastq mapping is done with hg19 index, use following command:

MethylPurify -f input.bam -b 300 -c 10 -s 50 -i methylpurify/db/CGI_hg19_slop1000.bed -g /path/to/hg19.fa --cnv

The results would be placed into input folder: alpha1.pred, MethylProfile.bed

Options

• -f: input BAM file

• -c: coverage level

• -b: genome bin size

• -s: sampling times

• -g: species genome fasta file

• -i: CG island specified, can use methylpurify/db/CGI_hg19_slop1000.bed for hg19, methylpurify/db/CGI_hg18_slop1000.bed for hg18

• –cnv: use cnv data or not, only available for hg19, for other assembly, do not use this