# #——风格,呼应= FALSE,结果=“隐藏”,消息= FALSE - - - - - - - - - - - - - - - - - - - - - - - - -库(BiocStyle)库(knitr)美元opts_chunk组(错误= FALSE,消息= FALSE,警告= FALSE) opts_chunk美元(图。asp = 1) # #——安装、呼应= TRUE, eval = FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # # #试试http://如果不支持https:// url # (!requireNamespace (“BiocManager”,悄悄地= TRUE)) # install.packages (BiocManager) # BiocManager::安装(“梅丽莎”)# # # #或下载从Github库# # install.packages (devtools) # devtools:: install_github (“andreaskapou /梅丽莎”build_vignettes = TRUE) # #——俾斯麦,eval = FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # #要求俾斯麦# bismark_methylation_extractor——全面——merge_non_CpG \ #——no_header——gzip bedGraph input_file。bam # #——binarise, eval = FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #库(Melissa) # # binarise scBS-seq数据# binarise_files (indir =“path_to_met_files_dir”) # #——compress_files, eval = FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # gzip文件名# #——melissa_data_obj,呼应= TRUE,消息= FALSE, eval = FALSE - - - - - - - - - - - - - - - - - - - # melissa_data <——create_melissa_data_obj (met_dir =“path_to_bin_met_dir”, # anno_file =“anno_file”, x = 3) # #——save_obj, eval = FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # saveRDS(文件= " melissa_data_obj。rds”, melissa_data) # #——filter_regions_by_coverage, eval = FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # melissa_data <——filter_by_cpg_coverage (melissa_data min_cpgcov = 10) # #——filter_regions_by_variability, eval = FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # melissa_data <——filter_by_variability (melissa_data min_var = 0.2) # #——filter_by_coverage_across_cells, eval = FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # melissa_data <——filter_by_coverage_across_cells (melissa_data # min_cell_cov_prcg = 0.5) # #——save_obj_filtered, eval = FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # saveRDS(文件= " melissa_data_obj_filtered。rds”, melissa_data) # # - - - - - eval = FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # # = = = = = = = = = = = = = = = = = # # 1。下载BAM数据# DATA_DIR = " . ./编码/ wgbs /“# #下载GM12878细胞系# wget - p $ {DATA_DIR} GM12878 / https://www.encodeproject.org/files/ENCFF681ASN/@@download ENCFF681ASN.bam # # #下载H1-hESC细胞系wget - p $ {DATA_DIR} H1hESC / https://www.encodeproject.org/files/ENCFF546TLK/@@download ENCFF546TLK.bam # # - - - - - eval = FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # DATA_DIR = "编码/ wgbs GM12878 / SRR4235788。bam“# out_dir = "编码/ wgbs / GM12878 /子样品/ GM12878 (" # (i = 1;我< = 40;+ + i)) # # my_command = " samtools视图- s $ {}。005 - b data_dir > {out_dir} _{我}美元。bam“# eval my_command美元# # # - - - - - eval = FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # data_dir = "编码/ wgbs GM12878 /子样品/ " # proc_dir = "编码/ wgbs / GM12878 /加工/ (" # (i = 1;我< = 40; ++i )) # do # my_command="bismark_methylation_extractor --ignore 2 --comprehensive --merge_non_CpG --no_header --multicore 4 -o $proc_dir --gzip --bedGraph ${data_dir}GM12878_${i}.bam" # eval $my_command # done ## ---- eval=FALSE-------------------------------------------------------------- # http://genome.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeHaibMethylRrbs ## ---- eval=FALSE-------------------------------------------------------------- # bismark_genome_preparation hg19/ ## ---- eval=FALSE-------------------------------------------------------------- # #================= # # 3. Run bismark # bismark --genome hg19/ encode/wgEncodeHaibMethylRrbsGm12878HaibRawDataRep2.fastq.gz # bismark --genome hg19/ encode/wgEncodeHaibMethylRrbsH1hescHaibRawDataRep2.fastq.gz ## ----session_info, echo=TRUE, message=FALSE----------------------------------- sessionInfo()