update readme

wbaopaul · Apr 29, 2022 · 1136c37 · 1136c37
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Showing 3 changed files with 6 additions and 6 deletions.
diff --git a/README.md b/README.md
@@ -240,7 +240,7 @@ Step by step guide to running scATAC-pro
                  -i output/summary
                  -c configure_user.txt
                  
-    ## merge peaks with qvlue < 0.01 and within 500bp distance of each other            
+    ## merge peaks with qvlue < 0.01 (be able to filtering by qvalue since v1.5.0) and within 500bp distance of each other            
     $ scATAC-pro -s mergePeaks
                  -i peak_file1,peak_file2,...,peak_fileN,500,0.01
                  -c configure_user.txt
@@ -431,7 +431,7 @@ See [here](https://scatacpro-in-r.netlify.app/note_module) or in your terminal:
                                  if reconstructMatrixPath not specified, a sub-folder reConstruct_matrix will be created
                                  under the same path as the input barcodes.txt file
           integrate: perform integration of two ore more data sets
-                           input: peak/feature files, a distance parameter and a qvalue cutoff separated by comma: peak_file1,peak_file2,200,0.01
+                           input: peak/feature files, a distance parameter and a qvalue cutoff separated by comma: peak_file1,peak_file2,...,peak_fileN,200,0.01
                            output: merged peaks, reconstructed matrix, integrated seurat obj and umap plot, saved in
                                    output/integrated/
           integrate_mtx: perform integration of two ore more data matrices given the reconstructed peak-by-cell matrix

diff --git a/configure_user.txt b/configure_user.txt
@@ -81,7 +81,7 @@ EmptyDrop_FDR = 0.001
 
 # set cutoff to define cell if CELL_CALLER is specified as FILTER
 # ignored if CELL CALLER was specified other than FILTER
-FILTER_BC_CUTOFF = --min_uniq_frags 3000 --max_uniq_frags 50000 --min_frac_peak 0.5 --min_frac_tss 0.0 --min_frac_promoter 0 --min_frac_enhancer 0.0 --max_frac_mito 0.1 --min_tss_escore 3
+FILTER_BC_CUTOFF = --min_uniq_frags 2000 --max_uniq_frags 60000 --min_frac_peak 0.5 --min_frac_tss 0.0 --min_frac_promoter 0 --min_frac_enhancer 0.0 --max_frac_mito 0.1 --min_tss_escore 1
 
 
 

diff --git a/scATAC-pro b/scATAC-pro
@@ -124,9 +124,9 @@ function help {
                          output: position sorted bam file in scATAC-pro format in output/mapping_result, mapping qc stat
                                  and fragment.txt file in output/summary/"
     echo "      mergePeaks: merge peaks (called from different data sets) if the distance is
-                            less than a given size in basepairs (200 if not specified) 
+                            less than a given size in basepairs (200 for instance),filtering peaks by qvalue 
                          input: peak files and a distance parameter separated by comma:
-                                peakFile1,peakFile2,peakFile3,200
+                                peakFile1,peakFile2,...,peakFileN,200,0.01
                          output: merged peaks saved in file output/peaks/merged.bed"
     echo "      reConstMtx: reconstruct peak-by-cell matrix given peak file, fragments.txt file, barcodes.txt and
                             an optional path for reconstructed matrix
@@ -136,7 +136,7 @@ function help {
                                  if reconstructMatrixPath not specified, a sub-folder reConstruct_matrix will be created
                                  under the same path as the input barcodes.txt file" 
     echo "      integrate: perform integration of two ore more data sets
-                           input: peak/feature files and a optional distance parameter, separated by comma: peak_file1,peak_file2,200
+                           input: peak/feature files and a optional distance parameter, separated by comma: peak_file1,peak_file2,...,peak_fileN,200,0.01
                            output: merged peaks, reconstructed matrix, integrated seurat obj and umap plot, saved in 
                                    output/integrated/"
     echo "      integrate_mtx: perform integration of two ore more matrices given the reconstructed peak-by-cell matrix