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 We can check the quality of the samples using Partek Genomics Suite before analyzing the data. 

Strand cross-correlation

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Checking the distribution of reads

BAM files contain both aligned and unaligned reads. The spreadsheet created during import shows the number of reads that were aligned to the reference genome. A large number of unaligned reads may be the result of poor quality sequencing data or alignment problems. It may also be useful to know how many reads map to more than one location in the genome if the options used during alignment supported multiple-mapped reads. 

• Select Alignments per read form the QA/QC section of the ChIP-Seq workflow (Figure 1)

A new spreadsheet named Alignment_Counts will be generated (Figure 2).