In the ChIP-Seq folder you will find another .fastq file called Control.fastq.
If you are not in there already, change into the data directory.
In [ ]:
cd data
Use the head command to look at this file:
In [ ]:
head Control.fastq
Use the information on the FASTQ Wikipedia page (http://en.wikipedia.org/wiki/FASTQ_format) to determine the quality encoding this FASTQ file is using. Then, adapting your commands to the quality encoding where needed, follow the steps you used to align the PAX5 sample to the genome and manipulate the SAM file in order to align the control reads to the human genome.
You can head back to visualising alignments in IGV or continue on to identifying enriched areas using MACS.