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README.md

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+# CCGA_circulome
+
+This repository contains code  from "Lv et al. Chromosomal, Extrachromosomal, and Transcriptomic Alternation Landscape in Urothelial Bladder Carcinoma".
+
+### Code
+
+#### obtain GC contents
+
+- **calGC.py**
+- **calGC.sh**
+
+#### obtain repeat ratios
+
+- **calReps.sh**
+- **calReps.py**
+
+#### some basic statistics
+
+- **calMappings_nochrM.py** obtain total mapping reads for each sample except chrM
+- **get_index_statistic.py** obtain total mapping ratio for each chromosome
+- **filter.py** filter raw eccDNA using some metrics 
+- **start_anno.jl** annotate eccDNA usings their start junction
+- **run_GISTIC2.sh** analyze total CNA characters from all samples
+- **getBreaks.jl** obtain all discordant break points from ecDNA graphs
+- **PABPC1_CIRCLE_RNA_WGS_alleleCount.sh** example for allelic frequency and coverage 
+
+#### scripts for main figure plots
+
+- **annotate_eccDNA_elements.plotData.R**
+- **B-allele_WGS_CircleSeq.plot.R**
+- **classify_samples_ecDNA.plotData.R**
+- **compare_eccDNA_abundance_heatmap.plot.R**
+- **compare_ecDNA_size_copy_BP.plotData.R**
+- **compare_EPM.plot.R**
+- **detected_chimeric_eccDNA.plotData.R**
+- **ecc_abundance_distribution.plot.R**
+- **ecc_map_genes.plotData.R**
+- **ecc_mRNA_cor.plot.R**
+- **ecc_mRNA_cor_rank.plot.R**
+- **eccNumbers_amp_noamp.plotData.R**
+- **EPM_diff_GSEA.plot.R**
+- **epm_mRNA_cor.plot.R**
+- **foldchange_amp_noamp.plot.R**
+- **genomic_dotplot_allele_frequency.plot.R**
+- **length_category_compare.plotData.R**
+- **length_distribution_eccDNA.plot.R**
+- **ligation_genes_exp_cor.plot.R**
+- **mRNA_ecDNA_eccDNA.plot.R**
+- **multiomicsViz.plot.R**
+- **oncoprint_for_BLCA_UBC.plot.R**
+- **PABPC1_circle_coverage.plot.R**
+- **statistic_for_BLCA_proportion.plotData.R**
+
+#### SV format and merge
+
+- **format_delly.jl**
+- **format_manta.jl**
+- **merge.manta.delly.py**
+
+### Contact
+If you have any questions concerning code or data, please do not hesitate to contact us at panxiaoguang@genomics.cn.