Question: Fw: [Galaxy-Bugs] Galaxy Tool Error Report From Bsib@Leeds.Ac.Uk
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Irene Bassano • 90 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
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modified 5.0 years ago
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Jennifer Hillman Jackson ♦ 25k
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5.0 years ago by
Irene Bassano • 90
