├── 1_trim25.bash ├── 2_novocode.bash ├── 3_bowtie.bash ├── 4_picard.bash ├── 5_remove_low_quality.bash ├── 6_size_Dist.bash ├── 7_size_classes.bash ├── 8_Homer.bash ├── GSE11431_Chen_Ctcf_mm10Peaks.txt ├── GSE11724_Young_Nanog_mm10_MergedPeaks.txt ├── GSE11724_Young_Oct4_mm10_Peaks.txt ├── GSE11724_Young_Sox2_mm10_MergedPeaks.txt ├── GSE14344_Crabtree_Brg1_mm10Peaks.txt ├── GSE31039_ENCODE_K27ac_mm10_regions.txt ├── GSE31039_ENCODE_K4me3_mm10_mergedRegions.txt ├── GSE49435_Ezh2_mm10Peaks.txt ├── README.md ├── mm10_bowtie2.header └── mybarcode.txt /1_trim25.bash: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sarahhainer/uliCUT-RUN/HEAD/1_trim25.bash -------------------------------------------------------------------------------- /2_novocode.bash: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sarahhainer/uliCUT-RUN/HEAD/2_novocode.bash 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