Question: How to upload a genome from igenomes to Galaxy?
0
gravatar for m.maleszewska
3.7 years ago by
Netherlands
m.maleszewska20 wrote:

As above - how can I directly upload a reference genome from http://cufflinks.cbcb.umd.edu/igenomes.html to a history at Galaxy?

Thank you in advance,

Best,

Monika

rna-seq tuxedo reference gtf • 1.4k views
ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by m.maleszewska20

I think I managed to upload a zipped file (tar), but how do I unpack it to be able to use it?

ADD REPLYlink written 3.7 years ago by m.maleszewska20

Thank you! The uploading worked, but I'm not sure if the unpacking did, as I have trouble using the file and the contents don't look right... It Autodetects it as a gtf, but I can't use it...

I think based on: ftp://ussd-ftp.illumina.com/README.txt , that it actually contains different sorts of files. Is there a way to extract all files at Galaxy, or I need to download it and upload back to Galaxy...?

ADD REPLYlink written 3.7 years ago by m.maleszewska20
1

If the archive contains more files Galaxy cannot unpack it automatically. Please do it manually. Sorry for the inconvenience.

ADD REPLYlink written 3.7 years ago by Martin Čech ♦♦ 4.5k

Thank you for the information!

Could you advise what source of genome is the best then to use with the Tuxedo pipeline at Galaxy? I at first uploaded a gtf file from UCSC with ensembl genes instead of one of igenomes, but in the end I missed the gene names in my CuffDiff output files, which was very inconvenient.. Please compare: https://www.biostars.org/p/107585/#108212 and Gene_short_name missing in CuffDiff output files .

Also, if I use merged.gtf file in my CuffDiff, what file should I use as Reference sequence (I now used Locally cached/hg_19, can it be part of the problem?)

I would very much appreciate some feedback on that... thank you!

All the best,

Monika

ADD REPLYlink written 3.7 years ago by m.maleszewska20

The cached reference genomes on the public Main Galaxy site, that match up best with the iGenomes files, are from UCSC. You will notice the short label as the same between the two sources. So, "hg19" in this case. And to supplement, the reference annotation file for hg19 is on the public Main Galaxy instance (http://usegalaxy.org) under: Shared Data -> Data Libraries -> iGenomes (along with the version for mm9). 

(Reposting key contents of other threads for readers finding this one instead.) Best, Jen, Galaxy team

ADD REPLYlink written 3.7 years ago by Jennifer Hillman Jackson24k
0
gravatar for Martin Čech
3.7 years ago by
Martin Čech ♦♦ 4.5k
United States
Martin Čech ♦♦ 4.5k wrote:

To upload file you hit the upload button (top left on the picture). Given the fact that your file is already on some other server you can tell Galaxy to directly download it from there - hit the Past/Fetch data button and enter the URL of the tar.gz file (you obtain the url of the file  by right clicking on the link at the cbcb.umd.edu site and selecting 'copy link'). Then you press start and you can close Galaxy if you wish. Galaxy will download it itself and unpack it automatically.

Picture: https://www.dropbox.com/s/8a7s53hfube2lf7/Screenshot%202014-08-01%2009.25.07.png

ADD COMMENTlink written 3.7 years ago by Martin Čech ♦♦ 4.5k
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