Hi there,
Could you please help me find my reference genome which is Mus Musculus so that I can map all chip seq data to reference genome? thank you!
Hi @Sherry
What Galaxy server do you use? What mapping tool do you use?
Public usegalaxy.* servers provide several indexed mouse genome assemblies. During setup of read mapping job type in search box for reference genomes “mouse” or Mus musculus, and you should see available genome assemblies.
Kind regards,
Igor
Hi Igor
Tnx so much for your reply to my question. Here I attached a screenshot for what I am doing in the galaxi as well as the server you were asking about. The version is 2.5.4+galaxy 0. I can’t find any reference genome name beyond the letter B. The choice starts as A. Melifera and finishes Biomhalaria glabrata.
Is there anything I did wrong? Please let me know.
Sherry
Here I am attaching another screenshot which shows clearly that there is no choice of “mice” in the available dropdown menu.
Hi @Sherry,
Thank you for the additional info. I see a URL in the 2nd screenshot. You use the ORG server. I can confirm that the ORG sever has several mouse genome assemblies indexed for bowtie2. Click at pull-down menu for genomes and type “mouse”, not “mice”. “Mus musculus” is also OK. Do you see the mouse genomes?
Kind regards,
Igor
Yes. I found it. I thought there was no way for me to type it but to choose from the menu. It actually allows me to type my choice. As soon as I typed mouse, the reference genome shows up. Thank you so much, Igor! very appreciate it!
Sherry
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