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balajtimate committed Nov 15, 2024
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6 changes: 3 additions & 3 deletions docs/guides/examples.rst
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Expand Up @@ -4,7 +4,7 @@ Examples
`HTSinfer` provides easy-to-use commands for analyzing single- and paired-ended RNA-Seq libraries.


Single-ended Library Example
Single-ended library example
----------------------------

To run `HTSinfer` on a single-ended RNA-Seq library, use the following command:
Expand All @@ -13,7 +13,7 @@ To run `HTSinfer` on a single-ended RNA-Seq library, use the following command:
htsinfer tests/files/adapter_single.fastq
Paired-ended Library Example
Paired-ended library example
----------------------------

To run `HTSinfer` on a paired-ended RNA-Seq library, use the following command:
Expand All @@ -24,7 +24,7 @@ To run `HTSinfer` on a paired-ended RNA-Seq library, use the following command:
Both commands will output the results in JSON format to :code:`STDOUT` and the log to :code:`STDERR`.

Example Output
Example output
--------------

Here is a sample output for the paired-ended library:
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2 changes: 1 addition & 1 deletion docs/guides/installation.rst
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Expand Up @@ -50,7 +50,7 @@ After the installation is complete, activate the :code:`htsinfer` Conda environm
conda activate htsinfer
Verify the Installation (Optional)
Verify the installation (optional)
----------------------------------

If you have installed the development or testing dependencies, you can verify that `HTSinfer` was installed correctly by executing the tests shipped with the package:
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4 changes: 2 additions & 2 deletions docs/guides/usage.rst
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Expand Up @@ -3,7 +3,7 @@ Usage

This section describes the general usage of `HTSinfer`.

General Usage
General usage
-------------

.. code-block:: bash
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The above command allows the user to infer metadata for single- or paired-ended RNA-Seq libraries by specifying file paths and relevant parameters. The tool outputs metadata in JSON format to :code:`STDOUT` and logs to :code:`STDERR`.

Command-line Options
Command-line options
---------------------

Available command-line parameters are categorized as follows:
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