I downloaded the data from GEO (GSE17972). It seems the data format is quite special one: qmap. Anyone have the script to transfer qmap bis-seq format To bigwig/wig/bedgraph.
GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17972 OR the question is same as: how to understand the qmap bis-seq format?
*Please ignore all the answer below. Since the reads were aligned to YH Genome, rather than GRCh37/38. I suggestion all the user who try to use this data should download the fastq and re-mappint to human genome, so that the result could be comparable with other dataset.*
* Download Finished, Alignment Finished, BW finished *
Okay. After all the guys' help. This problem has been totally solved.
1, this dataset is hg18 based.
2, qmap format has been listed by Devon Ryan..
3, in the qmap file, every base have been shown not only CpG, but every base.
4, therefore, when you calculate methylation level of CpG, you need extract the value for CpG sites.