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Initialize MACS2 in the BioHPC enviromentīedtools intersect -v -a ATAC_Rep1_peaks.narrowPeak -b sacCer3_blacklist.bed > ATAC_Rep1_peaks_filter.narrowPeakīedtools intersect -v -a ATAC_Rep2_peaks.narrowPeak -b sacCer3_blacklist.bed > ATAC_Rep2_peaks_filter.narrowPeak You may also need to restart IGV regularly if you are running with default memory allocations *Depending on the RAM and CPU of your computer, consider only viewing one coordinate. Processing of these files can yield BED/GFF peak files and continuous data such as bedGraph and bigWig files. This data represents the raw aligned data from the experiments. Open ChIP-seq_SRR5179211_Rep1.bam and ATAC-seq_Rep1_SRR7696734.bam and view the following genomic coordinates: It will automatically initialize on your system. Filter for 'sacCer3' and select this genome. The *.bai files are index files that are companion files to BAM files.Ĭlick the dropdown menu in the upper left and select 'more.'. Visualize ChIP-seq and ATAC-seq data in IGV On Windows computer, the software is installed in the directory C:\Program Files. Double click the IGV installation tool to install IGV. Go to the IGV web site ( ), click “Download”. virus protector, always click "no" to decline.ġ.3 Install IGV on your local workstation * The installer might prompt you to install other additional software, e.g. If you do not have any sftp client software on you laptop, download Filezilla client from this page. Unnessessary if you still have this installed from last week.įilezilla is a sftp client software. ġ.2 Install Filezilla client on your laptop