revised README

README.md

@@ -62,40 +62,40 @@ GETTING STARTED
 Below is an example for getting MIPgen up and running and designing probes to EGFR, TERT and BRAF
 
 first extract the tar file to make a MIPgen directory
-	tar -xf mipgen.tgz
+    tar -xf mipgen.tgz
 enter the directory to compile the source code
-	cd MIPGEN/
+    cd MIPGEN/
 use make to compile -- make sure you have a C++ compiler
-	make
+    make
 make a directory for practicing designs
-	mkdir ../mipgen_practice
-	cd ../mipgen_practice
+    mkdir ../mipgen_practice
+    cd ../mipgen_practice
 create a new file and type a list of gene symbols you would like to tile
 with MIPs
-	vim practice_genes.txt
+    vim practice_genes.txt
 you can use one of the scripts in the tools subdirectory and a refGene text
 file listing gene exons to pull out the genomic coordinates of your genes of
 interest
-	sh ../MIPGEN/tools/extract_coding_gene_exons.sh practice_genes.txt ../refGene.txt > practice_genes.bed
+    sh ../MIPGEN/tools/extract_coding_gene_exons.sh practice_genes.txt ../refGene.txt > practice_genes.bed
 check to make sure the coordinates are what you expect and that no errors
 occurred
-	less practice_genes.bed
+    less practice_genes.bed
 now you can perform designs with MIPgen
 here are some very basic options
 make sure you have the dependencies installed or accessible through a given
 path (BWA, tabix, samtools)
-	../MIPGEN/mipgen -regions_to_scan practice_genes.bed -project_name practice_design -min_capture_size 162 -max_capture_size 162 -bwa_genome_index $hg19ref
+    ../MIPGEN/mipgen -regions_to_scan practice_genes.bed -project_name practice_design -min_capture_size 162 -max_capture_size 162 -bwa_genome_index $hg19ref
 the final selection of MIPs is located in the picked MIPs file
 review the scores to make sure the MIPs stand a good chance of success
 (logistic scores below 0.6 are unlikely to provide usable data)
-	less practice_design.picked_mips.txt
+    less practice_design.picked_mips.txt
 by default all tested MIPs are output; this is a lot of output! (Turn it off with the silent_mode option)
-	rm practice_design.all_mips.txt
+    rm practice_design.all_mips.txt
 sai, fq (and sam) files are not deleted automatically and can also take up
 space
-	rm -f *.sai *.fq
+    rm -f *.sai *.fq
 generate a UCSC track with another tools script to visualize online
-	python ../MIPGEN/tools/generate_ucsc_track.py practice_design.picked_mips.txt practice_ucsc_track
+    python ../MIPGEN/tools/generate_ucsc_track.py practice_design.picked_mips.txt practice_ucsc_track
 look at the other files in this directory to see designs for TERT, BRAF and
 EGFR (we have not tested these designs experimentally so we cannot precisely
 assess predicted performance