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Diffstat (limited to 'README.md')
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1 files changed, 12 insertions, 1 deletions
@@ -19,6 +19,7 @@ PI: http://brisson.bio.upenn.edu/ * [Scoring Combinations](#score-combinations) * [Default Scoring Function](#default-scoring-function) * [Custom Scoring Function](#custom-scoring-function) +* [Filters](#filters) * [Output](#output) * [Select Mers](#select_merspy-output) * [Score Mers](#score_merspy-output) @@ -207,13 +208,23 @@ you can specify it like any other parameter like so: 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. + +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 + + + All mers -> ignore_mers -> ignore_all_mers -> average_binding -> non_melting -> consecutive_binding ## Output The file structure outputted by default is this: $foreground_$background └── run_1 # current_run - ├── filter # filter folder for filtering steps + ├── passes-filter # filter folder for filtering steps │ ├── 1-$foreground-ignore-mers │ ├── 2-$foreground-ignore-all-mers │ ├── 3-$foreground-average-binding |