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| -rw-r--r-- | README.md | 49 |
1 files changed, 32 insertions, 17 deletions
@@ -144,29 +144,44 @@ environmental variable if you wish to do so. The scoring function is this: fg_pts = all the points of each mer in the combination, and sequence ends4 - fg_mean_dist = mean distance between each point in fg_pts - fg_stddev = standard deviation of distance between each point in fg_pts + fg_mean_dist = mean distance between each point in fg_pts + fg_stddev = standard deviation of distance between each point in fg_pts - nb_primers = number of primers in a combination - primer_weight = extra weight for sets with higher primers + nb_primers = number of primers in a combination + primer_weight = extra weight for sets with higher primers - bg_ratio = length of background / number of times primer was in background + bg_ratio = length of background / number of times primer was in background mer_score = (nb_primers**primer_weight) * (fg_mean_dist * fg_std_dist) / bg_ratio ## Output The file structure outputted by default is this: - $foreground_$background/ - └── run_1 # current_run - ├── filter # filter folder for filtering steps - │ ├── 1-$foreground-ignore-mers - │ ├── 2-$foreground-ignore-all-mers - │ ├── 3-$foreground-average-binding - │ ├── 4-$foreground-non-melting - │ └── 5-$foreground-consecutive-binding - ├── $foreground-filtered-counts # final filtered mers used for selected_mers.py - ├── parameters # parameters used in the run - ├── selected-mers # final filtered mers used for selected_mers.py - └── scores-output # file outputted by score_mers.py + $foreground_$background + └── run_1 # current_run + ├── filter # filter folder for filtering steps + │ ├── 1-$foreground-ignore-mers + │ ├── 2-$foreground-ignore-all-mers + │ ├── 3-$foreground-average-binding + │ ├── 4-$foreground-non-melting + │ └── 5-$foreground-consecutive-binding + ├── $foreground-filtered-counts # final filtered mers used for select_mers.py + ├── parameters # parameters used in the run + ├── selected-mers # final filtered mers used for select_mers.py + └── scores-output # file outputted by score_mers.py +### select\_mers.py output + +Select mers outputs a tab delimited file, with 4 columns: mer foreground count +background count and the mer selectivity we give it. (higher is better) + + CTAACTTAGGTC 1572 155 10.14194 + CTAACATAGGTC 1479 132 11.20455 + GACCTATGTTAG 1479 132 11.20455 + + +### score\_mers.py output + +score medrs outputs a tab delmited file with 6 columns: + + nb_primers Combination Score FG_mean_dist FG_stdev_dist BG_ratio |