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Integrative Genome Viewer (IGV) is a free, downloadable desktop genome browser.  

Useful Resources

IGV website

IGV quick start guide

IGV user guide

1. Download IGV here You'll need an IGV account to do so. If you don't have one, register here
2. To load the reference genome and annotation (if not already pre-loaded),
   • File->Import Genome
   • Name your reference
   • Under Sequence file, provide a fasta file of the reference genome.  Though not required, it is also recommended to provide a gff file contain gene locations under Gene File.
   • Press 'Save'
3. To view one or more alignment files against the genome, you must have a sorted, indexed bam file for each sample.  Make sure to place both your .bam file and .bai files in the same location. For example, considering an alignment file V3BC01.bam (and its corresponding V3BC01.bam.bai)
   • File-> Load from File
   • Select the V3BC01.bam file.
   • If you have additional BAM files, load those as well. They will all be loaded as separate tracks.
4. If you have a SAM file, convert it to a sorted BAM file and index it.
   • To convert to BAM: samtools view -bS -o V3BC01.bam V3BC01.sam
   • To sort the BAM file: samtools sort V3BC01.bam V3BC01_sorted
   • To index the sorted BAM file: samtools index V3BC01_sorted.bam, which will generate the index V3BC01_sorted.bam.bai
5. Once all BAM files have been loaded, you may need to zoom in using the + button in the top hand corner to see the pileup of reads.  Other ways to traverse through the genome are:
   • Type the start and end coordinates on the coordinate window on top of the screen
   • Click on an exon/UTR on the gene annotation track or any other track loaded on the bottom
6. If you do not see any pileup of reads, 
   • Zoom in using the + button in the top hand corner
   • Make sure that the chromosome names in your genome and chromsome names in your bam file are the same.