modified: README.md

README.md

@@ -1 +1,33 @@
 # SMAPdigger
+
+## Step 1 (Setup softwares)
+
+1. Execute command "chmod +x ./*.sh"
+2. Execute command "./Software_Setup.sh"
+
+## Step 2 (Setup perl modules) 
+### If your cannot get access to administrator mode (Not recommanded)
+1, Execute command "./Module_Setup.sh <Perl module path (Absolute Full Path)>" in user mode
+2, Add the path of your perl module to environmental variable $PARL5LIB in file ~/.bashrc. For most linux system, it is usually something like "export PERL5LIB=$PERL5LIB:<Perl module path>/share/perl5/:<Perl module path>/lib64/perl5/".
+3, Execute command "source ~/.bashrc"
+### If your can get access to administrator mode (Strongly recommanded)
+1, Execute command "./Module_Setup.sh"
+## Step 3 (Data prepare)
+1, Download example file package "data.tar.gz" from ftp://public.genomics.org.cn/BGI/SMAP/ and save it to the root directory of SMAP. Extract the package with command "tar vxzf data.tar.gz"
+2, Put file "hg19.fa" into "./data/common" directory (It could also be downloaded from ftp://public.genomics.org.cn/BGI/SMAT/)
+3, Check if file "hg19.chr_len.bed" is in "./data/common" directory
+4, Check if file "CpGIsland.bed.seq.example" and "Upstream2k.bed.seq.example" are in "./data/element" directory
+5, Check if file adapter file and raw fq files  are in "./data/sample" directory
+6, Execute script "./Data_Prepare.sh" when use it first time.
+## Step 4 (Configure program) 
+1, modify configuration file "Eval.configure" 
+2, Execute script "perl ./Monitor.pl -c Eval.configure -o <Output path>"
+## Step 5 (Run program) 
+1, cd <Output path> 
+### If you want to run all the scripts by one step (Recommanded)
+2, Execute script “./SMAP_Run.sh"
+### If you want to run each script one by one
+2, Execute script "perl RRBS_prepare.pl"
+3, Execute script "perl RRBS_asm.pl"
+4, Execute script "perl RRBS_dmr.pl"
+5, Execute script "./RRBS_report.sh"