# Importing 10x Genomics .bcl Files

Partek Flow supports .bcl files based on 10x Genomics library preparation. The following document will guide you through the steps.

To start the import, create a new project and then select **Import Data > Import bcl files**. The *Import bcl* dialog will come up (Figure 1).

![Figure 1. Import bcl dialog](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-5db47fcee497d141e93a8881502071dde38cee4b%2FImport_bcl_dialog.png?alt=media)

Use the *Data directory* option to point to the location of the directory holding the data. It is located at the top level of the run directory and is typically labeled *Data*. Please see the tool tip for more info.

Use the *Run info file* option to point to the *RunInfo.xml* file. It is located at the top level of the run directory.

Use the *Sample sheet file* to point to the sample sheet file, which is usually a .csv file. Partek Flow can accept 10X Genomics' ["simple" and Illumina Experiment Manager (IEM) sample sheet format](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/mkfastq#example_data), which utilize 10X Genomics' sample index set codes. Each index set code corresponds to a mixture of four sample index sequences per sample. Alternatively, Partek Flow will also accept a sample sheet file that has been correctly formatted using the [sample sheet generator](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/bcl2fastq-direct) provided by 10X Genomics.

The click on the **Configure** link and make the following changes (Figure 2).

* *Min trimmed read length*: **8**
* *Mask short adapter reads*: **8**
* *Use bases mask*: see below
* *Create fastq for index reads*: **OFF**
* *Ignore missing bcls*: **ON**
* *Ignore missing filter*: **ON**
* *Ignore missing positions*: **ON**
* *Ignore missing controls*: **ON**

For the *Use bases mask* option, the read structure for Chromium Single cell 3' v2 prep kit is typically **Y26,I8,Y98.** The settings for Chromium Single cell 3' v3/v3.1 is typically **Y28,I8,Y91**. Please check the read structure detailed in the *RunInfo.xml* file and adjust the values to match your data.

![Figure 2. Setting the advanced options to import bcl files. The Use bases mask settings shown here are for Chromium v2 chemistry](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-036807f15cea7c22ae1e3461a48806998377806a%2Fimage2020-1-6_15-37-56.png?alt=media)

Click **Apply** to accept and then **Finish** to import your files.

## 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.