Several genome browsers exist to visualise the files generated during the analysis of high-troughput sequencing data, including BAM files. Two of the most popular tools are IGV and Tablet. In this practical we will be using IGV to visualise our BAM file. We can launch this tool from the Download section in the project website.
Once the interface is loaded, we can proceed to load the necessary files. In our case, we will load the following information:
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the reference genome:
Genomes > Load genome from file > reference/Drosophila_melanogaster.BDGP5.25.62.dna_rm.toplevel.fa -
the BAM file:
File > Load from file > data/mapped/untreated3.bam # IGV requires the BAM file to be indexed, which can be achieved with samtools # (i.e. `samtools index bam_file) # For this practical the index is already provided, so there is no need to run this command -
the annotation:
File > Load from file > reference/Drosophila_melanogaster.BDGP5.25.62.gtf
Exercise: Spend some time exploring the loaded BAM file and how the reads overlap with the known annotation. Can you find examples of split and spliced reads? For a subset of the reads, some nucleotides are highlighted in a different color. What do you think the explanation for this is? Hint: http://www.broadinstitute.org/igv/AlignmentData