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author | Calvin Morrison <mutantturkey@gmail.com> | 2014-03-26 21:05:25 -0400 |
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committer | Calvin Morrison <mutantturkey@gmail.com> | 2014-03-26 21:05:25 -0400 |
commit | 495228f7167a6df24a139022e7a0560a4dd07b56 (patch) | |
tree | ca163ce70968410ebbe30291c2c90aaec92da9b1 /README.md | |
parent | f6fe059e37d8e8ee0cb6f7acf72c8918473ad3f7 (diff) |
majorly rewrite and revamp the script to support runnign parts at a time
Diffstat (limited to 'README.md')
-rw-r--r-- | README.md | 11 |
1 files changed, 10 insertions, 1 deletions
@@ -19,7 +19,7 @@ Setup: Example Usage: - selectiveGenomeAmplification PfalciparumGenome.fasta HumanGenome.fasta; + SelectiveGenomeAmplification PfalciparumGenome.fasta HumanGenome.fasta; less PfalciparumGenome_HumanGenome/final_mers For user customizable variables: @@ -27,12 +27,21 @@ For user customizable variables: max_mer_distance=5000 max_select=6 min_mer_range=6 max_mer_range=12 \ SelectiveGenomeAmplification.sh PfalciparumGenome.fasta half.fasta + +By default SelectiveGenomeAmplification runs all four steps, but you can +specify the program to run other steps, like score in this example. + + current_run=run_1 SelectiveGenomeAmplification target.fasta bg.fasta score + +This function does not try to be smart, so use it wisely + ## Customizable variables range of mers, min and max variable | default | notes :---- | :---- | ---- | :---- +current\_run | Not Enabled | specify the run you want to run steps on min\_mer\_range | 6 | minimum mer size to use max\_mer\_range | 12 | maximum mer size to use max\_mer\_distance | 5000 | maximum distance between mers in foreground |