update readme and a missed package

wbaopaul · Mar 3, 2020 · c7491f4 · c7491f4
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Showing 8 changed files with 26 additions and 7 deletions.
diff --git a/4913 b/4913
diff --git a/README.md b/README.md
@@ -95,7 +95,7 @@ Dependencies
 -   trim\_galore (&gt;=0.6.3), Trimmomatic (&gt;=0.6.3)
 -   Regulratory Genomics Toolbox (RGT, for footprinting analysis, will ask whether you want to install it since the installation is done through conda, which takes a while and you may not want to conduct footprinting analysis)
 -   g++ compiler, bzip2, ncurses-devel
--   R packaages: devtools, flexdashboard, png, data.table, Matirx, Rcpp, ggplot2, flexmix, optparse, magrittr, readr, Seurat, bedr, gridExtra, ggrepel, kableExtra, viridis, RColorBrewer,pheatmap,motifmatchr, chromVAR, chromVARmotifs, SummarizedExperiment, BiocParallel, DESeq2, clusterProfiler, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, VisCello.atac
+-   R packaages: devtools, flexdashboard, png, data.table, Matirx, Rcpp, ggplot2, flexmix, optparse, magrittr, readr, Seurat, bedr, gridExtra, ggrepel, kableExtra, viridis, xlsx, RColorBrewer,pheatmap,motifmatchr, chromVAR, chromVARmotifs, SummarizedExperiment, BiocParallel, DESeq2, clusterProfiler, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, VisCello.atac
 
 Quick start guide
 -----------
@@ -241,6 +241,16 @@ Step by step guide to running scATAC-pro
 scATAC-pro -s visualize -i output/downstream_analysis/PEAK_CALLER/CELL_CALLER/VisCello_obj -c configure_user.txt
 
 ```
+- Note that the visualization can also be done through R/Rstudio:
+
+```
+devtools::install_github("qinzhu/VisCello", ref="VisCello-atac") ## install the package 
+
+library(VisCello.atac)
+
+cello('output/downstream_analysis/PEAK_CALLER/CELL_CALLER/VisCello_obj') ## launch VisCello in your web browser with prepared data
+```
+
 - More details about the visualization module can be found at [VisCello](https://github.com/qinzhu/VisCello/tree/VisCello-atac)
 
 Detailed Usage
@@ -395,6 +405,9 @@ $ singularity pull -F docker://wbaopaul/scatac-pro
 $ singularity run -H YOUR_WORK_DIR --cleanenv scatac-pro_latest.sif
 $ scATAC-pro --help
 
+## or using exec instead of run
+$ singularity exec -H YOUR_WORK_DIR --cleanenv scatac-pro_latest.sif scATAC-pro -s XXX -i XXX -c XXX
+
 ```
 
 3. To use it on HPC cluster:
@@ -412,13 +425,19 @@ singularity run -H YOUR_WORK_DIR --cleanenv scatac-pro_latest.sif
 scATAC-pro -s mapping -i fastq_file1,fastq_file2 -c configure_user.txt
 # and then qsub mapping.sh
 
+## or using exec instead of run
+singularity exec --cleanenv -H /mnt/isilon/tan_lab/yuw1/run_scATAC-pro/PBMC10k scatac-pro_latest.sif \ 
+scATAC-pro -s mapping -i fastq_file1,fastq_file2 -c configure_user.txt
 
 ```
 
 - **NOTE**: YOUR_WORK_DIR is your working directory, where the outputs will be saved and all data under YOUR_WORK_DIR will be available to scATAC-pro
 
 - **NOTE**: all inputs including data paths specified in configure_user.txt should be available under YOUR_WORK_DIR
 
+- **NOTE**: if running the *footprint* module, remember to download the reference data [rgtdata](https://chopri.box.com/s/dlqybg6agug46obiu3mhevofnq4vit4t) folder and put it under YOUR_WROK_DIR
+
+
 FAQs
 --------------
 - [How to proceed using 10x cellranger-atac output?](https://github.com/wbaopaul/scATAC-pro/wiki/FAQs)

diff --git a/scATAC-pro.wiki b/scATAC-pro.wiki
diff --git a/scripts/downstream.sh b/scripts/downstream.sh
@@ -36,7 +36,7 @@ wait
 
 ## go analysis
 if [ "$RUN_GO" = "TRUE" ]; then
-    ${curr_dir}/runGO.sh ${OUTPUT_DIR}/downstream_analysis/${PEAK_CALLER}/${CELL_CALLER}/differential_accessible_features_${group1}_VS_${group2}.txt $2 $3 &
+    ${curr_dir}/runGO.sh ${OUTPUT_DIR}/downstream_analysis/${PEAK_CALLER}/${CELL_CALLER}/differential_accessible_features_${group1}_vs_${group2}.txt $2 $3 &
 fi
 
 if [ "$RUN_Cicero" = "TRUE" ]; then

diff --git a/scripts/footprint_by_cluster.sh b/scripts/footprint_by_cluster.sh
@@ -46,7 +46,7 @@ fi
 prefix1=${prefix1/cluster_/}   ## absolute cluster name
 prefix2=${prefix2/cluster_/}
 
-input_peak=${down_dir}/differential_accessible_features_${prefix1}_VS_${prefix2}.txt
+input_peak=${down_dir}/differential_accessible_features_${prefix1}_vs_${prefix2}.txt
 
 if [ ! -e "$input_peak" ]; then
     echo "do DA..."

diff --git a/scripts/install/install_Rpackages.R b/scripts/install/install_Rpackages.R
@@ -5,7 +5,7 @@ if(!require(BiocManager)){
 }
 
 pks = c('devtools', 'flexdashboard', 'png', 'data.table', 'Matirx', 'Rcpp', 'ggplot2', 'flexmix',
-  'optparse', 'magrittr', 'readr', 'Seurat', 'bedr', 'gridExtra', 'ggrepel', 'kableExtra', 'viridis', 'writexl')
+  'optparse', 'magrittr', 'readr', 'Seurat', 'bedr', 'gridExtra', 'ggrepel', 'kableExtra', 'viridis', 'writexl', 'xlsx')
 
 for(pk in pks){
     if(!require(pk, character.only = T)) {

diff --git a/scripts/src/runDA.R b/scripts/src/runDA.R
@@ -113,6 +113,6 @@ setcolorder(markers, c('chr', 'start', 'end', 'p_val','avg_logFC','pct.1','pct.2
 
 #markers = markers[abs(avg_logFC) > 0, ]
 markers = markers[fdr <= 0.05, ]
-write.table(markers, file = paste0(output_dir, '/differential_accessible_features_', group1, '_VS_', group2, '.txt'), sep = '\t',
+write.table(markers, file = paste0(output_dir, '/differential_accessible_features_', group1, '_vs_', group2, '.txt'), sep = '\t',
             quote = F, row.names = F)
 
diff --git a/scripts/src/scATAC-pro_report.Rmd b/scripts/src/scATAC-pro_report.Rmd
@@ -396,7 +396,7 @@ if(file.exists(seurat_file)){
 ### GO Analysis
 ```{r, warning=F, message=F}
 go_file = paste0(down.dir, '/enrichedGO_differential_accessible_features_', group1, 
-                  '_VS_', group2, '.xlsx')
+                  '_vs_', group2, '.xlsx')
 if(file.exists(go_file)){
    #library(xlsx)
     cls = 1:length(unique(ss$active_clusters))