Yunhee Jeong 11 November 2021
MethylPurify detects differentially methylated regions (DMRs) and estimated tumour purity from tumor methylome bulk samples. Reference fasta file and the specification of CG island in .bed file are required to run this software. Details of the usage is available here: https://pypi.org/project/MethylPurify/#description
ref="./bismark/hg19.fa"
cpg_bed="./ref/CGI_hg19_slop1000.bed"
out_dir="./bulk_1/"
bin_size=200
coverage=10
sampling=50
MethylPurify -o $out_dir -f bulk_1.bam -b $bin_size -c $coverage -s $sampling -i $cpg_bed -g $ref --species "hg19"There are two output files. MethylProfile.bed contains detected DMRs information and alpha1.pred shows the estimated tumour purity.
cat MethylProfile.bed## #chr start end m1 m2 read_count cytosine_count_in_CG likelihold
## chr1 13146 13346 0.527089433533726 0.548177745041164 21 3 -24.131789023097646
## chr1 13349 13549 0.5189147967934834 0.9306057259456227 49 4 -66.78750195158416
## chr1 13556 13756 0.8809747309632764 0.8741802410686826 34 4 -51.37477183232292
## chr1 13759 13959 0.9967528407511198 0.9334398255438524 33 2 -7.942365830938414
## chr1 14544 14744 0.9928236929072323 0.9368540977469867 20 7 -23.946534988654783
cat alpha1.pred ## 0.255
## 6244