10 months ago by
Hello - Where are you using Galaxy? At Galaxy Main (http://usegalaxy.org) or elsewhere?
SAM/BAM data uploaded will have the datatype autodetected and assigned if the settings are left at default. Double checking that this datatype assignment was actually made is the first place to check for a problem. A SAM dataset could have a datatype of tabular assigned, but a BAM dataset will only be allowed to have that datatype assigned (if all is working correctly).
If this occurred at Galaxy Main, we'll want to investigate. If this is occurring in a local Galaxy, perhaps Samtools needs to be installed.
Let us know more about the situation and we can follow up from there. Thanks! Jen, Galaxy team