--- a
+++ b/b_DownstreamAnalysisScript/downloadData.R
@@ -0,0 +1,74 @@
+
+# MESSAGE -----------------------------------------------------------------
+# 
+# author: Yulin Lyu
+# email: lvyulin@pku.edu.cn
+# 
+# require: R whatever
+# 
+# ---
+
+# * Load packages ---------------------------------------------------------
+
+library(tidyverse)
+library(magrittr)
+library(glue)
+
+# * From GEO --------------------------------------------------------------
+
+setwd("/mnt/f") # download dir
+
+# RNA
+setwd("exampleData/RNA/raw")
+geo <- "GSE147839"
+sra <- "SRP254790"
+bioProj <- "PRJNA622253"
+
+# ATAC
+setwd("exampleData/ATAC/raw")
+geo <- "GSE157237"
+sra <- "SRP279550"
+bioProj <- "PRJNA660602"
+
+# download from SRA directly using wget (slow)
+
+dir.create("sra")
+
+download.file(
+  glue("http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?save=efetch&db=sra&rettype=runinfo&term={sra}"),
+  glue("{where}/{sra}.csv", where = getwd()))
+
+projMeta <- read_csv(glue("{where}/{sra}.csv", where = getwd()))
+
+srr <- projMeta$Run
+downPath <- projMeta$download_path
+
+down_cmd <- glue("wget -b -c -o sra/{srr}.log -O sra/{srr}.sra {downPath}")
+
+write.table(c("#!/bin/bash\n", down_cmd), "down.sh", sep = "\n", quote = F, row.names = F, col.names = F)
+
+# download from ENA using aspera (fast)
+# NOTE: NOT all datasets in SRA are accessible in ENA
+
+# <todo> I will complete this part when needed in the future.
+
+
+# * From ArrayExpress -----------------------------------------------------
+
+# <todo> I will complete this part when needed in the future.
+
+
+# * Extract fastq ---------------------------------------------------------
+
+dir.create("fastq")
+
+ext_cmd <- glue("fasterq-dump -e 10 -3 -O fastq sra/{srr}.sra")
+
+write.table(c("#!/bin/bash\n", ext_cmd), "ext.sh", sep = "\n", quote = F, row.names = F, col.names = F)
+
+gzip_cmd <- glue(
+  "gzip fastq/{srr}.sra_1.fastq &
+  gzip fastq/{srr}.sra_2.fastq &")
+
+write.table(c("#!/bin/bash\n", gzip_cmd), "gzip.sh", sep = "\n", quote = F, row.names = F, col.names = F)
+