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  • Program to view multiple alignment files at once

    I have aligned reads to a database containing 10 reference sequences using BWA MEM, and now have .sam and .bam files.

    Is there a program that would allow me to few those 10 alignments within the one .sam/.bam file all at once?

    I am currently using Tablet, but this only allows me to view the alignment for each reference sequence one at a time.

    Alternatively, is there a program that would allow me to view multiple .sam/.bam files at once, when each of those .sam/.bam files have only 1 reference sequence?

    I'm sorry if this question has been answered before but I couldn't find a post that answered this for me.

    Thank you for your help.

  • #2
    Are you sure about tablet not being able to open more than one alignment?

    In any case IGV will allow you to open multiple files (aligned to same genome). You will need to make sure you have enough RAM available and change the startup script for IGV to make more RAM available as needed.

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