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| -rw-r--r-- | README.md | 4 |
1 files changed, 3 insertions, 1 deletions
@@ -37,10 +37,12 @@ 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/.counts | directory for counts directory +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 | ignore_mers | Not Enabled | mers to explicitly ignore, space seperated ex. ignore_mers="ACAGTA ACCATAA ATATATAT" +Y | foreground | path of foreground file +Y | background | path of background file |