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Fix886 #905

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Jan 17, 2020
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Documentation fixes, closes #886
dpryan79 committed Jan 17, 2020

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This commit was created on GitHub.com and signed with GitHub’s verified signature.
commit 04c9786c39341071fc2fd03582a9839d99037bed
2 changes: 1 addition & 1 deletion deeptools/computeMatrixOperations.py
Original file line number Diff line number Diff line change
@@ -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',
4 changes: 2 additions & 2 deletions deeptools/parserCommon.py
Original file line number Diff line number Diff line change
@@ -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)'

5 changes: 4 additions & 1 deletion docs/content/tools/computeMatrix.rst
Original file line number Diff line number Diff line change
@@ -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
^^^^^^^^

4 changes: 2 additions & 2 deletions galaxy/wrapper/deepTools_macros.xml
Original file line number Diff line number Diff line change
@@ -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)