add figures

henssen-lab · May 27, 2024 · 50af255 · 50af255
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diff --git a/.gitignore b/.gitignore
@@ -1,4 +1,5 @@
 # ignore data folder
+data/figures
 data/ecDNA_reconstruction/
 data/ecDNA_mixtures/
 data/simulation_benchmarking/

diff --git a/README.md b/README.md
@@ -67,7 +67,7 @@ Additionally, the reconstruction and de-novo assembly for cell lines are compare
 
 # 5. Paper figures
 
-Go to [figures](docs/figures.md)
+Go to `../data/figures`.
 
 
 ## Citation

diff --git a/docs/compare_shasta_decoil.md b/docs/compare_shasta_decoil.md
@@ -1,4 +1,4 @@
-### 4.2.1 Perform de-novo assembly for cell lines using Shasta
+### 4.3 Perform de-novo assembly for cell lines using Shasta
 
 ```
 conda create env -f scripts/shasta/assembly.yaml
@@ -10,8 +10,10 @@ sbatch shasta_v6.0.6.sh <tr14_fastq> ../../../data/ecDNA_comparison/tr14/shasta_
 sbatch shasta_v6.0.6.sh <sta-nb-10dm_fastq> ../../../data/ecDNA_comparison/sta-nb-10dm/shasta_v6.0.6
 ```
 
-### 4.2.1 Compare Decoil and Shasta outputs against the against published ecDNA structures
+### 4.4 Compare Decoil and Shasta outputs against the against published ecDNA structures
 
 ```
 bash run ../ecDNA_comparison/comparison_reconstruction_true.sh
-```
+```
+
+Output is under `../data/ecDNA_comparison/`.
diff --git a/docs/figures.md b/docs/figures.md
diff --git a/docs/properties.md b/docs/properties.md
diff --git a/docs/reconstruction_celllines_patients.md b/docs/reconstruction_celllines_patients.md
@@ -60,12 +60,12 @@ This is available also as docker container [madagiurgiu25/decoil:1.1.2-slim](htt
 ### 4.2.2 Run reconstruction for cell lines
 
 ```bash
-sbatch ../ecDNA_reconstruction/celllines/run_decoil_v112_07022024_slurmarray_celllines_hg19.sh
-sbatch ../ecDNA_reconstruction/celllines/run_decoil_v112_07022024_slurmarray_celllines_hg38.sh
+sbatch ../ecDNA_reconstruction/run_decoil_v112_07022024_slurmarray_celllines_hg19.sh
+sbatch ../ecDNA_reconstruction/run_decoil_v112_07022024_slurmarray_celllines_hg38.sh
 ```
 
 ### 4.2.3 Run reconstruction for patient samples
 
 ```bash
-sbatch run_decoil_v112_07022024_slurmarray.sh
+sbatch ../ecDNA_reconstruction/run_decoil_v112_07022024_slurmarray.sh
 ```
diff --git a/ecDNA_comparison/assemblyviz.R b/ecDNA_comparison/assemblyviz.R