diff --git a/.gitignore b/.gitignore
deleted file mode 100755
index eb5fcf84681fac0504a38531ade2a93c48b05b71..0000000000000000000000000000000000000000
--- a/.gitignore
+++ /dev/null
@@ -1,7 +0,0 @@
-example/input/data/
-example/input/PWMScan/
-example/input/referenceGenome/
-doc/Documentation.odt
-*/.snakemake/
-example/output/
-example/input/output/
diff --git a/.gitignore~ b/.gitignore~
deleted file mode 100755
index fac871d90bbc71aa2740a9b648e0685b7ce42390..0000000000000000000000000000000000000000
--- a/.gitignore~
+++ /dev/null
@@ -1,6 +0,0 @@
-example/input/data/
-example/input/PWMScan/
-example/input/referenceGenome/
-doc/Documentation.odt
-.snakemake/
-/example/output/
diff --git a/doc/.nfs0000000bce7de20400000003 b/doc/.nfs0000000bce7de20400000003
deleted file mode 100644
index ef7863f2eb68af5a509139081ddf4abf3a97c18b..0000000000000000000000000000000000000000
Binary files a/doc/.nfs0000000bce7de20400000003 and /dev/null differ
diff --git a/doc/Documentation.pdf b/doc/Documentation.pdf
index d3fda6eb598a1e556d098ce47b63a11c3063b506..ccf61665d4d4a6ce6a064fc7c91990279475ab15 100644
Binary files a/doc/Documentation.pdf and b/doc/Documentation.pdf differ
diff --git a/src/Snakefile b/src/Snakefile
index 5cec68e0c97f1998aa26a2cd6ec450959bbc1b0f..e2331c4c5f8d99e52bdbdf906e52a41a2775e823 100644
--- a/src/Snakefile
+++ b/src/Snakefile
@@ -280,7 +280,7 @@ rule intersectPeaksAndBAM:
         genomeFile2  = rules.idxstatsBAM.output.genomeFile2,
         bam        = lambda wildcards: getBamFileFromBasename(wildcards.basename)
     output:
-        peaksOverlap = PEAKS_DIR + '/' + compType + '{basename}.' + peakFileEndingPattern,
+        peaksOverlap = PEAKS_DIR + '/' + compType + '{basename}' + peakFileEndingPattern,
         resortedBed  = TEMP_DIR  + '/' + compType + '{basename}.' + "resorted.gz"
     log:
     message: "{ruleDisplayMessage} Run intersect and count for file {input.consensusPeaks} with {input.bam}..."