revised README

README.md

@@ -61,53 +61,53 @@ 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
+First extract the tar file to make a MIPgen directory
 
     tar -xf mipgen.tgz
 
-enter the directory to compile the source code
+Enter the directory to compile the source code
 
     cd MIPGEN/
 
-use make to compile -- make sure you have a C++ compiler
+Use make to compile -- make sure you have a C++ compiler
 
     make
 
-make a directory for practicing designs
+Make a directory for practicing designs
 
     mkdir ../mipgen_practice
     cd ../mipgen_practice
 
-create a new file and type a list of gene symbols you would like to tile
+Create a new file and type a list of gene symbols you would like to tile
 with MIPs
 
     vim practice_genes.txt
 
-you can use one of the scripts in the tools subdirectory and a refGene text
+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
 
-check to make sure the coordinates are what you expect and that no errors
+Check to make sure the coordinates are what you expect and that no errors
 occurred
 
     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)
+Now you can perform designs with MIPgen!
+Here is a design with 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
 
-the final selection of MIPs is located in the picked MIPs file
+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
 
-by default all tested MIPs are output; this is a lot of output! (Turn it off with the silent_mode option)
+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
 
@@ -116,13 +116,13 @@ space
 
     rm -f *.sai *.fq
 
-generate a UCSC track with another tools script to visualize online
+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
 
-look at the other files in this directory to see designs for TERT, BRAF and
+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
+assess predicted performance for these probes)
 
 
 © University of Washington 2014