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  • IGV bam file

    Hi,

    I've two alignment of short reads in bam format. In one sample I've a lot of alignment in one position of the sequence ( ~ 100000 reads aligned ) and in the other sample I've, in the same position, very few aligned reads ( ~ 100 ).

    When I load the two bam files in IGV, I wanted to compare (visually) the two alignment. The problem is that the y axis scale is different for the two track and it seems that the two samples have the same number of aligned reads.

    Here's a picture


    Uploaded with ImageShack.us

    How can I have the same scale for the two coverage ?

    Thanks

    N.

  • #2
    Right clicking the coverage track gives you some options - if you deselect "Autoscale" you can select "Set Data Range" and manually enter the range.

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