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Question: Uploading Illumina Bam Files In Galaxy
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gravatar for Priya Bhatt
5.7 years ago by
Priya Bhatt • 40
Priya Bhatt • 40 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? Furthermore are there any examples/workflows available that others have created when using Illumina data Thank you! Best, Priya
galaxy • 1.2k views
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modified 5.7 years ago by Jennifer Hillman Jackson ♦ 25k • written 5.7 years ago by Priya Bhatt • 40
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gravatar for Jennifer Hillman Jackson
5.7 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
Hello Priya, 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 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 -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org
ADD COMMENT • link written 5.7 years ago by Jennifer Hillman Jackson ♦ 25k
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