>BSprepare("/Users/aamu_user/Desktop/DMR_pipe/ancestor_output/ancestor_reads.fastq_bismark_sorted_CpG.txt","/Users/aamu_user/Desktop/DMR_pipe/ancestor_output/", tabix="/Users/aamu_user/Downloads/tabix-0.2.6")
Error in all_files[[i]] : subscript out of bounds
You are just using it wrongly... BSprepare requires just the location of the folder containing text files with methylation information....so the correct way would be following:
BSprepare("/Users/aamu_user/Desktop/DMR_pipe/ancestor_output/","/Users/aamu_user/Desktop/DMR_pipe/ancestor_output/", tabix="/Users/aamu_user/Downloads/tabix-0.2.6")
Thank you Bharati and Kamal. The only problem I'm having is that my meth.call() step creates a .txt file with these chr names, "Pt" "Mt" "4" "2" "3" "5" "1". I also did a similar analysis on the same data using Methyl-Kit and "Pt" "Mt" still came up. Do you think its a problem with my samtools? I'm using version 3.2.2
Check your fastq files. Chromosome nomenclature within them is propagated further in downstream analysis by any software you use.
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