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.
On 11/27/13 12:56 PM, Irene Bassano wrote:
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
(sorry, I think i sent a mail to bugs report by mistake)
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