Data for this tutorial can be downloaded from the Partek website using this link - ChIP-Seq tutorial data. To follow this tutorial, download the two .bam files and unzip them on your local computer using 7-zip, WinRAR, or a similar program. 

• Store the 2 .bam files at C:\Partek Training Data\ChIP-Seq or to a directory of your choosing. We recommend creating a dedicated folder for the tutorial on a local drive. 
• Select ChIP-Seq from the Workflows drop-down menu (Figure 1)
  
  

• Select Import and Manage Samples from the Import section of the ChIP-Seq workflow
• Select Browse... or use the file tree to navigate to the folder where you stored the .bam files

All .bam files in the folder will be selected by default (Figure 2). 

• Verify that chip.bam and mock.bam are selected
• Select OK

The Sequence Import dialog will launch (Figure 3). This allows us to choose the output file name and destination for the parent spreadsheet, as well as the species, and genome build of the imported samples. By default, the output file destination is the folder the .bam files are located. 

• Set Output file to ChIP-Seq 
• Set Species to Homo sapiens using the drop-down menu
• Set Genome build tohg18 using the drop-down menu
• Select OK

The Bam Smaples Manager dialog will open (Figure 4). This dialog can be used to add samples to the project (Add samples), remove samples (Remove samples), to associate multiple files with particular samples (Manage samples), and to map the chromosome names form the input files to the association files (Manage sequence names). 

• Select Close 

You may see the Sort bam files dialog. If so, select OK. The imported spreadsheet will open after import completes (Figure 5). In this spreadsheet, samples are rows and the number of aligned reads is listed in column 2. Number of Alignments.