From a62836a32af8785db02b5f6bcbd1dfb777d6148e Mon Sep 17 00:00:00 2001 From: wbaopaul Date: Mon, 20 Apr 2020 14:17:21 -0400 Subject: [PATCH] update readme --- README.md | 8 +++----- job_pub2 | 0 scripts/install/install_dependencies.sh | 4 ++-- scripts/src/runDA.R | 2 +- 4 files changed, 6 insertions(+), 8 deletions(-) delete mode 100644 job_pub2 diff --git a/README.md b/README.md index 23d71be..40d3b6f 100644 --- a/README.md +++ b/README.md @@ -48,7 +48,7 @@ Updates ------------ - Current version: 1.1.1 - March, 2020 - * *get_mtx* requires two fragments.txt and peak file, separated by comma + * *get_mtx* requires two input files: a fragments.txt file and a peak file, separated by comma * annotate peak as overlapped with a gene Tss if the corresponding distance <= 1000bp; mark peak with a gene if their distance <= 100kb - Feb, 2020 * *integrate* module enables 3 options: seurat, harmony and pool @@ -61,7 +61,6 @@ Updates * added new parameters in the configuration file: Top_Variable_Features, REDUCTION, nREDUCTION * enabled all clustering methods mentioned in the manuscript, along with kmeans clustering on principal components * file path changed to like downstreame_analysis/PEAK_CALLER/CELL_CALLER/..., indicating peak caller - * qc_per_barcode requires two input files, separated by comma, see example and detailed usage - Jan, 2020 * added a new module *mergePeaks* to merge different peak files called from different data sets * added a new module *reConstMtx* to reconstruct peak-by-cell matrix given a peak file, a fragment file and a barcodes.txt file @@ -82,7 +81,7 @@ Dependencies ### Programming language users should install -- R (>=3.6.0) +- R (>=3.6.1) - Python (>=3.6.0) ### Software packages required @@ -445,5 +444,4 @@ FAQs Citation -------------------------------------- -Yu W, Uzun Y, Zhu Q, Chen C, Tan K. *scATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing data.* bioRxiv.org; 2019 -doi: https://doi.org/10.1101/824326 +Yu W, Uzun Y, Zhu Q, Chen C, Tan K. [*scATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing data.*](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02008-0) Genome Biology; 2020 diff --git a/job_pub2 b/job_pub2 deleted file mode 100644 index e69de29..0000000 diff --git a/scripts/install/install_dependencies.sh b/scripts/install/install_dependencies.sh index 18def54..733f279 100755 --- a/scripts/install/install_dependencies.sh +++ b/scripts/install/install_dependencies.sh @@ -152,9 +152,9 @@ if [ $? != "0" ]; then exit 1; else pver=`R --version 2>&1 | head -1 | cut -d" " -f3` - vercomp $pver "3.6.0" + vercomp $pver "3.6.1" if [[ $? == 2 ]]; then - echo -e "$RED""R v3.6.0 or higher is needed [$pver detected].""$NORMAL" + echo -e "$RED""R v3.6.1 or higher is needed [$pver detected].""$NORMAL" exit 1; fi fi diff --git a/scripts/src/runDA.R b/scripts/src/runDA.R index edcd64e..7a75489 100644 --- a/scripts/src/runDA.R +++ b/scripts/src/runDA.R @@ -95,6 +95,6 @@ setcolorder(markers, c('chr', 'start', 'end', 'p_val','avg_logFC','pct.1','pct.2 'p_val_adj', 'fdr', 'cluster', 'peak', 'peak0')) 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_', args[3], '_vs_', args[4], '.txt'), sep = '\t', quote = F, row.names = F)