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The picture below shows a fully expanded BAM file, showing the difficulty of seeing any details. The second picture shows just the depth graph (*BAM *track is 'hidden').

Depth Graph (Start)

Depth Graph (Start) only graphs the first nucleotide of each read. This is most useful when assessing coverage bias in RNA-Seq or other high-throughput sequencing experiments. Often some regions are better represented than others, thanks to PCR amplification bias or other artifacts.

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Mismatch Graph

The Mismatch graph is specific to short read alignment files, such as BAM.  The graph shows only the number of mismatched nucleotides across all reads at a specific genomic location, which can be very helpful in the detection of allelic variation, SNP identification and also error checking. Right click in the label to access the menu; choose Track Operations > Mismatch Graph. This function requires that the genomic sequence be loaded; if it is not loaded, IGB will load the sequence for you.

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