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:
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 :
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