From cdca14fd202156d0e6a4f437ee5cd535e53b8d6e Mon Sep 17 00:00:00 2001 From: "EVAN A. BOYLE" Date: Thu, 19 Jun 2014 12:38:33 -0700 Subject: [PATCH] revised README --- README.md | 32 ++++++++++++++++---------------- 1 file changed, 16 insertions(+), 16 deletions(-) diff --git a/README.md b/README.md index 8d14a5d..eac2940 100644 --- a/README.md +++ b/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