Question: Fw: [Galaxy-Bugs] Galaxy Tool Error Report From Bsib@Leeds.Ac.Uk
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gravatar for Irene Bassano
4.9 years ago by
United Kingdom
Irene Bassano90 wrote:
Hi Jen, thanks. I am a bit confused: on Galaxy the only human genome listed is hg_g1k_v37. So when I uploaded the new data from "Get data", under "Genome" I selected hg_g1k_v37 Now, all i want is to get cufflinks with gene names: which genome am I supposed to use? the only one I knew was hg19 from iGenomes...but seems i cannot use it. Do I have to select a genome when I upload raw fastq data? I havent stated doign anything so far, its just raw data Thanks a lot, Irene ________________________________________ To: Irene Bassano Cc: galaxy-bugs@bx.psu.edu Subject: Re: [galaxy-bugs] Galaxy tool error report from bsib@leeds.ac.uk Hello, iGenomes covers the UCSC build, and this named "Human Feb. 2009 (GRCh37/hg19) (hg19)" in the full name in the UI. The "hg19" key is the important part - as the name may be abbreviated in some tools, but this key will be in all. The genome with the "hg_g1k_v37" key is slightly different and you will have another genome mismatch problem with the RNA-seq (and most other) tools if you combine this genome with data from UCSC (the source of hg19) or the wrong iGenomes file. "hg_g1k_v37" (source: 1000 genomes via GATK) and "hg19" (source: UCSC) are just about the same, but the identifiers are different. If you want to examine the differences, both are available on our rsync server and can be downloaded and compared. On the "Help -> Support" wiki are links for reference genomes. The iGenomes GTF file for hg19 is on the public Main server, if that is more convenient for you, or should you just want to be sure you have the right one. Look in Shared Data -> Data Libraries -> iGenomes. Best, Jen Galaxy team ps. please try to send new questions to one of our lists, thanks! -- Jennifer Hillman-Jackson http://galaxyproject.org
rna-seq cufflinks • 979 views
ADD COMMENTlink modified 4.9 years ago by Jennifer Hillman Jackson25k • written 4.9 years ago by Irene Bassano90
0
gravatar for Jennifer Hillman Jackson
4.9 years ago by
United States
Jennifer Hillman Jackson25k wrote:
Hello Irene, Are you using the public Main Galaxy instance at http://usegalaxy.org? And the tool "Get Data -> Upload File"? Following these instructions (there is a video): http://wiki.galaxyproject.org/Support#Loading_data Typing "human" in the " Genome:" box should bring up the hg* choices. Please check and let us know. Jen Galaxy team -- Jennifer Hillman-Jackson http://galaxyproject.org
ADD COMMENTlink written 4.9 years ago by Jennifer Hillman Jackson25k
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