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Question: Uploading fastq files
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gravatar for gkuffel22
2.9 years ago by
gkuffel22 • 170
United States
gkuffel22 • 170 wrote:

Hi,

This will be an easy one...when uploading fastq files to Galaxy is it important to associate a Database/Build with each sample and why?  Thank you in advance.
galaxy • 746 views
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modified 2.9 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.9 years ago by gkuffel22 • 170
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gravatar for Jennifer Hillman Jackson
2.9 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Assigning the build will just help with organizing the data for most tools, but some do interpret this metadata and use it (many Picard tools work this way). Plus, assigning at upload is less tedious than clicking into the individual dataset pencil icons and assigning after.

Be sure to assign the correct type. Simply using "fastq" is ok if you do not know if the data is "fastqsanger" yet (what most tools require). If all data are similar, upload one, test to see if  "fastqsanger" can be directly applied, or if running the FastqGroomer is required. Here is how to check: https://wiki.galaxyproject.org/Support#FASTQ_Datatype_QA

Good question, will help others to use Galaxy efficiently and avoid input format problems (it really is the most common reason for tool errors based on my experience). Jen, Galaxy team
ADD COMMENT • link modified 2.9 years ago • written 2.9 years ago by Jennifer Hillman Jackson ♦ 25k
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