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readme change to specify fasta for genome reference
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EVAN A. BOYLE committed Aug 7, 2014
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Expand Up @@ -104,7 +104,7 @@ 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
../MIPGEN/mipgen -regions_to_scan practice_genes.bed -project_name practice_design -min_capture_size 162 -max_capture_size 162 -bwa_genome_index ${hg19_fasta}

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
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