Question: Adding reference genome to Galaxy
0
gravatar for tylertibetli
12 weeks ago by
tylertibetli0 wrote:

Hi, I want to add reference genome(hg19) from UCSC main table to my Galaxy account,how can I do that?I want to realign my reads and when I try to use GATK realigner,it asks reference genome.

alignment galaxy • 123 views
ADD COMMENTlink modified 12 weeks ago • written 12 weeks ago by tylertibetli0
1
gravatar for Jennifer Hillman Jackson
12 weeks ago by
United States
Jennifer Hillman Jackson24k wrote:

Hello,

The GATK tools hosted at https://usegalaxy.org are from a very old version (1.4) and have been deprecated for some time now. These are natively indexed for hg_g1k_v37 (1000 Genomes) and not hg19 (UCSC). Using hg19 from the history as a custom reference genome will cause several to fail for exceeding memory resources. We strongly recommend that you avoid using these tools.

Instead, please see the variant analysis tutorials here that include the most current tools and methods:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 12 weeks ago by Jennifer Hillman Jackson24k
0
gravatar for tylertibetli
12 weeks ago by
tylertibetli0 wrote:

Hi Jen,

Thank you for your assistance.

ADD COMMENTlink written 12 weeks ago by tylertibetli0
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