Question: Uploading Illumina Bam Files In Galaxy
gravatar for Priya Bhatt
5.7 years ago by
Priya Bhatt40
Priya Bhatt40 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
ADD COMMENTlink modified 5.7 years ago by Jennifer Hillman Jackson25k • written 5.7 years ago by Priya Bhatt40
gravatar for Jennifer Hillman Jackson
5.7 years ago by
United States
Jennifer Hillman Jackson25k 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: 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 : Best, Jen Galaxy team -- Jennifer Hillman-Jackson Galaxy Support and Training
ADD COMMENTlink written 5.7 years ago by Jennifer Hillman Jackson25k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 172 users visited in the last hour