# QA/QC, data processing, and dimension reduction
### QA/QC & Data Processing
Once the data has been imported in the project we can start pre-processing the data:
We will first remove all non-expression features in the data (e.g. NegProbes).
* Click on *Filtering > Filter features* from the menu on the right
* Select *Metadata* and set the task settings as follows
* Click **Finish**
In the Analyses tab
* Click on the resulting filtered counts node
* Select *QA/QC > Single cell* QA/QC from toolbox, once the task has completed we can open the report by double-clicking the node:
We will remove the cells with low counts and number of detected features.
* Click on *Select & Filter* and set lower threshold to 50 for both (remember that this is data-dependent and will change based on your dataset)
* Click Filter include
* Click *Apply observation filter* to the filtered counts node:
Click on the node generated by the filtering task in the Analyses tab.
* Click *Filtering > Filter features.* Apply a noise reduction filter:
We can now normalize our filtered data.
* Click *Normalization and scaling > Normalization.* Use the recommended settings by clicking :
### Data Exploration
Now that we have filtered low quality cells and normalized our data, we can start clustering to identify cell populations.
* Click on the normalized data node
* From the menu on the right select *Exploratory analysis > PCA.* We are going to use the top 2000 features by variance and calculate the first 50 principal components (PCs):
Once the PCA has run, click on the PCA result node in the Analyses tab.
* Select *Exploratory analysis > UMAP* from the toolbox. Set the UMAP parameters as follows:
* Top **20** PCs
* Local neighborhood size **60**
* Minimal distance **0.20**
While the UMAP is running we can also queue a clustering task. Click on the PCA result node in the Analyses tab, select *Exploratory analysis > Graph-based clustering.*
* We are going to use the Leiden algorithm to cluster our data (make sure to select the radio button for it)
* Set the number of PCs to **10**
* In the advanced settings, set the resolution parameter to **8e-5** and click **Apply**:
\\
### Additional Assistance
If you need additional assistance, please visit [our support page](http://www.partek.com/support) to submit a help ticket or find phone numbers for regional support.
