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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--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
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use the Galaxy Development list:
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please use the interface at:
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