Hi Lilach, Yes, BAM files are sorted and indexed when they are uploaded. Just load the .bam, not the .bam.bai when using FTP. Sorry for the delayed reply! Jen Galaxy team On 8/25/13 3:14 AM, lilach noy wrote:

hello all,

Does anyone know if in order to use Slice bam I need to sort the bam file first or does galaxy automatically sort any bam file uploaded?

Many thanks, Lilach Noy

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