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===Calculate MHL loads and construct matrices.=== *I wrote a script to calculate the "methylated haplotype load (MHL)" for all targets in a hapInfo file, and construct MHL matrices for all files in a folder: [[Media:get_methHapLoad_matrix.txt|get_methHapLoad_matrix.pl]]. *Five MHL matrices were generated. **1407-combined_RRBS_mld_blocks_stringent_mhl_matrix.txt: All RRBS data sets generated in July 2014 **140917_dRRBS_mld_blocks_stringent_mhl_matrix.txt: Additional dRRBS data sets generated in Sept 2014. Noi used two enzymes (MspI+TaqI) for the digestion. **141216_SeqCap_mld_blocks_stringent_mhl_matrix.txt: NimbleGen SeqCap data on WGBS libraries, this data set has low enrichment factor due to sub-optimal capture condition. The WGBS libraries were good, so the data are useful. **150209_SeqCap_mld_blocks_stringent_mhl_matrix.txt: NimbleGen SeqCap data on WGBS libraries, generated in Feb 2015. Both WGBS libraries and capture experiments were good. **150209_BSPP_mld_blocks_stringent_mhl_matrix.txt: BSPP capture data on WGBS libraries, generated in Feb 2015. **N37_10_tissue_pool_mhl_matrix.txt: Low-coverage WGBS data from ten human tissues. **N37_10_tissue_pool_WB_WGBS_mld_blocks_stringent_mhl_matrix.txt: Low-coverage WGBS data from ten human tissues, plus whole blood WGBS data. *Merge these matrices into two bigger matrices ../merge_mhl_matrix.pl N37_10_tissue_pool_WB_WGBS_mld_blocks_stringent_mhl_matrix.txt 141216_SeqCap_mld_blocks_stringent_mhl_matrix.txt 150209_SeqCap_mld_blocks_stringent_mhl_matrix.txt 150209_BSPP_mld_blocks_stringent_mhl_matrix.txt > N37_WB_WGBS_SeqCap_BSPP_merged__mld_blocks_stringent_mhl_matrix.txt ../merge_mhl_matrix.pl N37_10_tissue_pool_WB_WGBS_mld_blocks_stringent_mhl_matrix.txt 1407-combined_RRBS_mld_blocks_stringent_mhl_matrix.txt 140917_dRRBS_mld_blocks_stringent_mhl_matrix.txt > N37_WB_WGBS_RRBS_dRRBS_merged__mld_blocks_stringent_mhl_matrix.txt
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