diff options
| author | Calvin Morrison <mutantturkey@gmail.com> | 2014-04-02 13:59:18 -0400 |
|---|---|---|
| committer | Calvin Morrison <mutantturkey@gmail.com> | 2014-04-02 13:59:18 -0400 |
| commit | 8bfd592cdb052396a8ca087919c20afc5f998ef2 (patch) | |
| tree | 2cd3549e6b348809d49b6b512ca21b1786eb6a8b | |
| parent | 7361823d6c1a94d497d80b98202b24c075435e87 (diff) | |
move some table stuff, add sortby param
| -rw-r--r-- | README.md | 11 |
1 files changed, 6 insertions, 5 deletions
@@ -156,16 +156,16 @@ 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 +min\_melting\_temp | 0° | minimum melting temp of mers +max\_melting\_temp | 30° | maximum melting temp of mers +min\_foreground\_binding\_average | 50000 | eliminate mers that appear less frequently than the average (length of foreground / # of occurrances) +ignore\_mers | Not Enabled | mers to explicitly ignore, space separated ex. ignore\_mers="ACAGTA ACCATAA ATATATAT" +ignore\_all\_mers\_from\_files | Not Enabled | ignore any mers found in these files. space separated. output\_directory | $foreground\_$background/ | ex. if fg is Bacillus.fasta and bg is HumanGenome.fasta then folder would be $PWD/Bacillus.fasta\_HumanGenome\_output.fasta/ counts\_directory | $output\_directory/.tmp | directory for counts directory tmp\_directory | $output\_directory/.tmp | temporary files directory -max\_melting\_temp | 30° | maximum melting temp of mers -min\_melting\_temp | 0° | minimum melting temp of mers -min\_foreground\_binding\_average | 50000 | eliminate mers that appear less frequently than the average (length of foreground / # of occurrances) max\_select | 15 | maximum number of mers to pick max\_check | 35 | maximum number of mers to select (check the top #) -ignore\_mers | Not Enabled | mers to explicitly ignore, space separated ex. ignore\_mers="ACAGTA ACCATAA ATATATAT" -ignore\_all\_mers\_from\_files | Not Enabled | ignore any mers found in these files. space separated. foreground | Not Enabled | path of foreground file background | Not Enabled | path of background file max\_consecutive\_binding | 4 | The maximum number of consecutive binding nucleotides in homodimer and heterodimers @@ -173,6 +173,7 @@ fg\_weight | 0 | How much extra weight to give higher frequency mers in fg. see primer\_weight | 0 | How much extra weight to give to sets with a higher number of primers. (between 0 and 1) output\_top\_nb | 10000 | How many scores do you want to output in your sorted output file? score\_func | Not Enabled | see the [custom scoring](#custom-scoring-function) section +sort\_by | max | How do you want to rank top-scores? min means smaller is better, max is larger. 'min' or 'max' ## Equations |