External data (extdata) source and preprocessing

The data found in the extdata directory are derived from the paper, The RON Receptor Tyrosine Kinase Promotes Metastasis by Triggering MBD4-Dependent DNA Methylation Reprogramming. The associated data has been uploaded to the Gene Expression Omnibus (GEO) with the GEO Accession number GSM127125.

MCF7_Cunha_header_only.vcf.gz(.tbi) and MCF7_Cunha_chr11p15.bed.gz(.tbi)

WGBS data accessed from the GEO link above was aligned to the hg19 genome using biscuit version 1.3.20160324. The output VCF was converted to a BED file (using biscuit vcf2bed) and then chromosome 11p15 (chr11p15) was selected as the data is purely for example purposes. Following the reduction to chr11p15, the BED file was gzipped and tabixed using bgzip and tabix, which are available through samtools. Due to the large size of the corresponding VCF file, the header of the file was selected out using the command line tool head (head -n 125 vcf_file.vcf). This reduced file was then gzipped and tabixed in the same way as the BED file.

MCF7_Cunha_shuffled_header_only.vcf.gz(.tbi) and MCF7_Cunha_chr11p15_shuffled.bed.gz(.tbi)

The "shuffled" versions of the MCF7 Cunha BED and VCF files are derived from the corresponding BED and VCF files described previously. This was done as these files are merely to produce examples of biscuiteer capabilities and are not to be used in a normal analysis. With that in mind, the VCF file was modified from the original by changing out references to "MCF7_Cunha" with "MCF7_Cunha_shuffled". The BED file was generated with the code found in scripts/ Please see the code for documentation on how the shuffled BED file was created. Once the shuffled VCF and BED files were generated, they were gzipped and tabixed for use in biscuiteer.

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biscuiteer documentation built on Nov. 8, 2020, 8:28 p.m.