Extract Genomic DNA not recognizing mm9

[rtrumbly]

Trying to run Extract Genomic DNA on bed file with mm9 as genome. The tool says no options available for locally cached reference genome. when I edit the file to hg19 genome, it is recognized, but not for mm9 which is the correct genome. I have attached a screenshot of the problem. Here is a screen shot of the problem.

[mvdbeek]

That means there is no index installed for mm9. I would suggest contacting the administrator of the Galaxy instance you are using. If that is not an option you can upload a fasta file for the mm9 genome and change "Choose the source for the reference genome" to history and select your fasta file with the genome sequence.

[jennaj]

Hello @rtrumbly

If you are working at Galaxy Main https://usegalaxy.org, please use bedtools GetFastaBed instead. It performs the same basic function plus has more options. You will find mm9 and many other genomes indexed.

[rtrumbly]

Jennifer, Thanks for your help, that solves my problem. Bob Trumbly From: Jennifer Hillman-Jackson <notifications@github.com> Sent: Wednesday, February 19, 2020 12:36 PM To: galaxyproject/galaxy <galaxy@noreply.github.com> Cc: Trumbly, Robert <Robert.Trumbly@utoledo.edu>; Mention <mention@noreply.github.com> Subject: [EXTERNAL] Re: [galaxyproject/galaxy] Extract Genomic DNA not recognizing mm9 (#9396) Hello @rtrumbly<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_rtrumbly&d=DwMCaQ&c=heEcP2AsrLOv4XP8e7I9NA&r=IiQjGnnOf_ab8bT2M6V994poMcyQqUipJAcAcG9Iy2M&m=l-FRFvr2oeCiuzvcWV0HPwt-KID0Arj-iStK5ARJ2qY&s=Yvg8YSReOHfRy3A7lKOAWwMw055D3MeXD2KDgjKgVbU&e=> If you are working at Galaxy Main https://usegalaxy.org<https://urldefense.proofpoint.com/v2/url?u=https-3A__usegalaxy.org&d=DwMCaQ&c=heEcP2AsrLOv4XP8e7I9NA&r=IiQjGnnOf_ab8bT2M6V994poMcyQqUipJAcAcG9Iy2M&m=l-FRFvr2oeCiuzvcWV0HPwt-KID0Arj-iStK5ARJ2qY&s=jmipMEJZH9yA9rEXTA0KqBvLmNtEyCv-XUkvnhoyCOs&e=>, please use bedtools GetFastaBed instead. It performs the same basic function plus has more options. You will find mm9 and many other genomes indexed. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_galaxyproject_galaxy_issues_9396-3Femail-5Fsource-3Dnotifications-26email-5Ftoken-3DACM4UNG4JRI6KBLLKJBOOV3RDVUZNA5CNFSM4KX3DFLKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMIXJ3A-23issuecomment-2D588346604&d=DwMCaQ&c=heEcP2AsrLOv4XP8e7I9NA&r=IiQjGnnOf_ab8bT2M6V994poMcyQqUipJAcAcG9Iy2M&m=l-FRFvr2oeCiuzvcWV0HPwt-KID0Arj-iStK5ARJ2qY&s=Dv6yAPOjWcZ7RYUAcU8MIdL7Nldv_PURqcCYgKbj1PQ&e=>, or unsubscribe<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ACM4UNBE7PZECQJTVTJLNX3RDVUZNANCNFSM4KX3DFLA&d=DwMCaQ&c=heEcP2AsrLOv4XP8e7I9NA&r=IiQjGnnOf_ab8bT2M6V994poMcyQqUipJAcAcG9Iy2M&m=l-FRFvr2oeCiuzvcWV0HPwt-KID0Arj-iStK5ARJ2qY&s=Qp3pFiXNNZfR_e0ukhbauhDtjZraKs_2Hk8yLPObLYQ&e=>.