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| author | Calvin Morrison <mutantturkey@gmail.com> | 2014-04-08 13:43:45 -0400 |
|---|---|---|
| committer | Calvin Morrison <mutantturkey@gmail.com> | 2014-04-08 13:43:45 -0400 |
| commit | 1b49a2d276a62546e4e9522e26228265142066a3 (patch) | |
| tree | 96abe4dfb6ae106ebd5bdaae1cb46b017b7a5118 /README.md | |
| parent | 927b681691b293afbb798a65d4340446e7f6fb6c (diff) | |
more docs and add strand
Diffstat (limited to 'README.md')
| -rw-r--r-- | README.md | 24 |
1 files changed, 21 insertions, 3 deletions
@@ -230,11 +230,17 @@ You need to use **valid** python code. ## Filters -There are several filters that our mers go through, to eliminate ones that won't fit our needs. They are all configurable via the tunable parameters. If you look in a output directory, you'll see a folder called "passes-filter". This contains a file for each of the different steps in the pipeline, and the contents of each file is what 'passes' that filter. +There are several filters that our mers go through, to eliminate ones that +won't fit our needs. They are all configurable via the tunable parameters. If +you look in a output directory, you'll see a folder called "passes-filter". +This contains a file for each of the different steps in the pipeline, and the +contents of each file is what 'passes' that filter. -For example, if you ignored the mer 'AAAAA', then in passes-filter/1-$foreground-ignore-mers there would be no line containing that. +For example, if you ignored the mer 'AAAAA', then in +passes-filter/1-$foreground-ignore-mers there would be no line containing that. -The filter system works like a big pipe, whatever gets filtered out won't make it to the next step. the order is like this +The filter system works like a big pipe, whatever gets filtered out won't make +it to the next step. the order is like this All mers -> ignore_mers -> ignore_all_mers -> average_binding -> non_melting -> consecutive_binding @@ -272,3 +278,15 @@ background count, and the mer selectivity value. (higher is better) score mers outputs a tab delimited file with 6 columns: nb_primers Combination Score FG_mean_dist FG_stdev_dist BG_ratio + +## Post Processing + +To get a more detailed look at each scored combination we provide the +output\_full\_genome.py script. This script will output all of the points in a +selected set along with some metadata, including position, what sequence it is in, +what strand and what mer it is. + + output_full_genome.py -f fg.fa -s fg.fa_bg.fa/run_12/top-scores -n 15 -o sets + +this will output one file for eat of the the top 15 sets in top-scores, in the +folder sets. |