diff --git a/deeptools/computeMatrixOperations.py b/deeptools/computeMatrixOperations.py
index 60d1e3630..a67cdd7a2 100644
--- a/deeptools/computeMatrixOperations.py
+++ b/deeptools/computeMatrixOperations.py
@@ -269,7 +269,7 @@ def sortArgs():
     optional.add_argument('--transcriptID',
                           default='transcript',
                           help='When a GTF file is used to provide regions, only '
-                          'entries with this value as their feature (column 2) '
+                          'entries with this value as their feature (column 3) '
                           'will be processed as transcripts. (Default: %(default)s)')
 
     optional.add_argument('--transcript_id_designator',
diff --git a/deeptools/parserCommon.py b/deeptools/parserCommon.py
index 929ac9b22..073953126 100644
--- a/deeptools/parserCommon.py
+++ b/deeptools/parserCommon.py
@@ -165,7 +165,7 @@ def gtf_options(suppress=False):
 
     if suppress is False:
         help = 'When a GTF file is used to provide regions, only \
-        entries with this value as their feature (column 2) \
+        entries with this value as their feature (column 3) \
         will be processed as transcripts. (Default: %(default)s)'
 
     group.add_argument('--transcriptID',
@@ -174,7 +174,7 @@ def gtf_options(suppress=False):
 
     if suppress is False:
         help = 'When a GTF file is used to provide regions, only \
-        entries with this value as their feature (column 2) \
+        entries with this value as their feature (column 3) \
         will be processed as exons. CDS would be another common \
         value for this. (Default: %(default)s)'
 
diff --git a/docs/content/tools/computeMatrix.rst b/docs/content/tools/computeMatrix.rst
index ba11c5f02..60aaf8cb5 100644
--- a/docs/content/tools/computeMatrix.rst
+++ b/docs/content/tools/computeMatrix.rst
@@ -10,7 +10,7 @@ computeMatrix
    :nodefault:
 
 Details
-^^^^^^^^^^^^^^^
+^^^^^^^
 
 ``computeMatrix`` has two main modes of use:
 
@@ -44,6 +44,9 @@ The following tables summarizes the kinds of optional outputs that are available
 .. attention::
    As of version 3.0, computeMatrix produces output with labels present for each sample. Matrices produced with that or later versions can not be used with older versions of ``plotHeatmap`` or any other deepTools program.
 
+.. note::
+   ``computeMatrix`` will properly handle strand information if your BED file includes that column (GTF files always include strand). For the ``--metagene`` option to work, you will need either a BED12 (including columns 11 and 12) or a GTF file as input. GFF is NOT the same as GTF format!
+
 Examples
 ^^^^^^^^
 
diff --git a/galaxy/wrapper/deepTools_macros.xml b/galaxy/wrapper/deepTools_macros.xml
index 8bc50cc4a..8547c77ef 100644
--- a/galaxy/wrapper/deepTools_macros.xml
+++ b/galaxy/wrapper/deepTools_macros.xml
@@ -217,10 +217,10 @@
             help="If set and a BED12 or GTF file or files is used to provide regions, only exons will be used. This is convenient for looking at coverage over mature mRNA transcripts or similar uses where introns should be ignored." />
         <param argument="--transcriptID" optional="True" value="transcript" type="text"
             label="transcript designator"
-            help="When a GTF file is used to provide regions, only entries with this value as their feature (column 2) will be processed as transcripts. Default: transcript" />
+            help="When a GTF file is used to provide regions, only entries with this value as their feature (column 3) will be processed as transcripts. Default: transcript" />
         <param argument="--exonID" optional="True" value="exon" type="text"
             label="exon designator"
-            help="When a GTF file is used to provide regions, only entries with this value as their feature (column 2) will be processed as exons. CDS would be another common value for this. Default: exon" />
+            help="When a GTF file is used to provide regions, only entries with this value as their feature (column 3) will be processed as exons. CDS would be another common value for this. Default: exon" />
         <param argument="--transcript_id_designator" optional="True" value="transcript_id" type="text"
             label="transcriptID key designator"
             help="Each region has an ID (e.g., ACTB) assigned to it, which for BED files is either column 4 (if it exists)