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| -rw-r--r-- | README.md | 21 |
1 files changed, 11 insertions, 10 deletions
@@ -33,16 +33,17 @@ range of mers, min and max C | variable | default | notes :---- | :---- | :---- | ---- | :---- -Y | min_mer_range | 6 | minimum mer size to use -Y | max_mer_range | 10 | maximum mer size to use -Y | max_mer_distance | 5000 | maximum distance between mers in foreground -N | output_directory | $PWD/$foreground_$background/ | ex. if fg is Bacillus.fasta and bg is HumanGenome.fasta then folder would be $PWD/Bacillus.fasta_HumanGenome_output.fasta/ -Y | counts_directory | $output_directory/.tmp | directory for counts directory -Y | tmp_directory=$output_directory/.tmp | temporary files directory -Y | max_melting_temp | 30° | maximum melting temp of mers -Y | min_melting_temp | 0° | minimum melting temp of mers -Y | min_mer_count | Not Enabled (0) | only select mers that occur more frequently than this number -Y | max\_select | maximum number of mers to pick +Y | min\_mer\_range | 6 | minimum mer size to use +Y | max\_mer\_range | 12 | maximum mer size to use +Y | max\_mer\_distance | 5000 | maximum distance between mers in foreground +N | output\_directory | $PWD/$foreground\_$background/ | ex. if fg is Bacillus.fasta and bg is HumanGenome.fasta then folder would be $PWD/Bacillus.fasta\_HumanGenome\_output.fasta/ +Y | counts\_directory | $output\_directory/.tmp | directory for counts directory +Y | tmp\_directory=$output\_directory/.tmp | temporary files directory +Y | max\_melting\_temp | 30° | maximum melting temp of mers +Y | min\_melting\_temp | 0° | minimum melting temp of mers +Y | min\_mer\_count | Not Enabled (0) | only select mers that occur more frequently than this number +Y | max\_select | |maximum number of mers to pick +Y | max\_check | |maximum number of mers to select (check the top #) Y | ignore\_mers | Not Enabled | mers to explicitly ignore, space seperated ex. ignore\_mers="ACAGTA ACCATAA ATATATAT" Y | foreground | Not Enabled | path of foreground file Y | background | Not Enabled | path of background file |