Bugfix and documentation

doc/output.md

@@ -6,25 +6,27 @@ This output has grown in an organic fashion, for which I apologize.
 
 
 
-`report/`
+### `report/`
 
 An HTML report. 
 
 Note that this contains symlinks to other files in the directory, so when copying it make sure to dereference symlinks (eg `cp -L`).
 
-`plotter_config.json`
+
+
+### `plotter_config.json`
 
 JSON file containing various useful pieces of information, intended for visualization software that uses the pipeline output directory.
 
 
 
-`peaks/relation-child.gff`
+### `peaks/relation-child.gff`
 
 Peaks called from poly(A) reads. Really only the 3' end of these features is meaningful, the 3' end is the polyadenylation site.
 
 
 
-`samples/<samplename>/`
+### `samples/<samplename>/`
 
 Per-sample files.
 
@@ -36,7 +38,7 @@ The `samples/<samplename>-polyA` directories contain BAM files limited to reads
 
 
 
-`raw/`
+### `raw/`
 
 Read count and tail length statistics in CSV format. These are also given as a .zip file in the html report.