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Created with Raphaël 2.2.09Feb10Dec9714Sep11Dec15Oct24Sep231811328Aug27167424Jul20161593123Junworkflowr set upmastermasterset upStart workflowr project.annotatedannotations updatedchange filenameadded annotationsclean upchange foldersrearranging scriptsnew SSH keyduplicate fileupdatedfirst commitadded chainCleanerupdatedadded links to scripts for lastz ad repeak maskerfirst commitgenerate commands to run array scripts for lastz and repeatMaskerchanged directory name to ouput peak calls for 10M reads per samplechanged directory to call peaks on 10M readsedited snakemake commandfirst commit - subsample BAM files to the desired read numberfirst commit - script parses a multiFASTA and output a separate fasta file for each sequence headerfirst commit of conda environment with packages for whole genome alignmentadded repeat masking stepsaltered to run on 10M subsampled BAM filesfirst commit. script to subsample BAM files in a directoryedit input/output folders to run peak calling pipeline on subsampled BAM filesadded -snakefile flag to command to call a specific snakefilecreated separate config files for each histone markcreated separate snakefiles for histone marks as I couldn't get the wildcards to work so had to hardcode one of the rulesadded info on converting to 2bit formatrule for calculating frip in replicate peaksadded merged inputadded input controladding merging of input control BAM filesadded frip for comparing replicate peaks to pooled peakscommented out to fix bug laterchange directory