Hi Irene,
This is a repeat of what I sent you on the other list, but may be informative for others, too, so it seemed worth posting here.
...
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
On 11/27/13 12:56 PM, Irene Bassano wrote:
Hi Jen, I uploaded some fastq files and selected as Genome from the drop down list ""Homo sapiens b37(hg_g1k_v37).
Is this the same as the genome listed in UCSC "February 2009 (GRCh37/hg19)"?
I am using iGenomes to get the gene names rather than annotation such as NM_00xxxx and I fused the UCSC website choosing the newest genome, February 2009
Thanks,
(sorry, I think i sent a mail to bugs report by mistake)
best, Irene ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
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