Hello Priya,

On 3/28/13 3:32 PM, Priya Bhatt wrote:
Dear Galaxy Users,

I had a quick question as a new Galaxy user.  I just received WGS data from Illumina where I'm given .bam files.  I am not given .fastq files.  Most of the Galaxy tutorials I've seen online have started with raw data in .fastq format.  Can Galaxy handle if I were to upload a .bam file using the "Get Data" tool?

Yes, BAM files are used in Galaxy. If you intend to map though, converting to FASTQ would be a first step. Using the tool search at the top of the left tool panel, enter "SAM", then scroll down to the tool " SAM to FASTQ". Once coverted, the data may or may not need to be Groomed before using it:
http://wiki.galaxyproject.org/Support#Dataset_special_cases


Furthermore are there any examples/workflows available that others have created when using Illumina data
Many of the tutorials involve Illumina data. The "Shared Data" tab will point to both Workflow and Pages shared by the core team and community. Also see "Help -> Video tutorials".

Try this search to find Q&A about user/scientific topics :
http://galaxyproject.org/search/mailinglists/

Best,

Jen
Galaxy team


Thank you!

Best,
Priya



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