Hi Lilach - This tool won't work on compressed formats like BAM. Would it make sense in your analysis to convert both inputs to SAM format first, then run the tool? There are tools to merge BAM files, or compare intervals to BAM files, but these are not really the same thing. If you want to share more about the end goal - and the first suggestion won't work - maybe we can figure out method with more details (list or private). Thanks! Jen Galaxy team On 8/29/13 12:15 AM, lilach noy wrote:

Hello all,

I am having troubles with the Subtract Whole Dataset function - i've tried subtracting one BAM file from another and got as an output a bai file. I need it to be a BAM file so i can convert it to SAM and see the data in a none binary form. Anyone have any thoughts on the issue?

Thank you for trying :) Lilach

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