Hi Lilach,
Regarding the cloud instance, you can load data from the public main
instance of Galaxy just like any other URL. On the "Get Data -> Upload
Data" form on your cloud instance , paste in the URLs of the datasets
from main. The URL can be captured by right-clicking on a dataset's disk
Hello Lilach,
The genome build 'hg_g1k_v37' is build "b37" in the GATK documentation.
Hg19 is also included (as a distinct build). I encourage you to examine
these if you are interested in crossing over between genomes or
identifying other projects that have data based on the same genome build
May I join to the question of Carlos? what is exactly hg_g1k_v37? and how
can I get the intervals of specific genes in this format?
Thanks,
Lilach
2012/6/27 Lilach Friedman
> Hi Jennifer,
> Is there a way to directly upload my files from the public Galaxy to my
> cloud Galaxy instance (in AW
Hi Jennifer,
Is there a way to directly upload my files from the public Galaxy to my
cloud Galaxy instance (in AWS)? Or should I download them first to my
computer, and then to upload them? (It takes a lot of time because of the
low uploading speed).
Thanks,
Lilach
2012/6/26 Jennifer Jackson
Hi Lilach,
Sorry for the late response. Jen just confirmed the disadvantages of
my approach. I don't know how difficult could be for you to double
check the coordinates you have in your interval file are correct for
hg_g1k_v37. If you feel confident they will work and want to proceed,
you could do
Hello Lilach,
Currently, the human reference genome indexed for the GATK-beta tools is
'hg_g1k_v37'. The GATK-beta tools are under active revision by our team,
so we expect there to be little to no change to the beta version on the
main public instance until this is completed.
Attempting to
Hi Carlos,
Thank you very much for this explanation.
The format of my intervals file is:
chr133289059732890664NM_59_cds_1_0_chr13_32890598_f0+chr1332893213
32893462NM_59_cds_2_0_chr13_32893214_f0+chr133289921232899321
NM_59_cds_3_0_chr13_32899213_f0+chr133290023732900287
NM_59_cds
On Thu, Jun 21, 2012 at 10:50 AM, Lilach Friedman wrote:
> Hi Jennifer,
> Thank you for this reply.
>
> I made a new BWA file, this time using the hg19(full) genome.
> However, when I am trying to use DepthOfCoverage, the reference genomr is
> stucked on the hg_g1k_v37 (this is the only option to
Hi Jennifer,
Thank you for this reply.
I made a new BWA file, this time using the hg19(full) genome.
However, when I am trying to use DepthOfCoverage, the reference genomr is
stucked on the hg_g1k_v37 (this is the only option to select), and I cannot
change it to hg19(full). Most probably, because
If hg_g1K_v37 == "1000 Genomes version of GRCh37" then it is the GRCh37
Primary assembly + a decoy sequence to try to soak up off target reads.
The chromosome coordinates are the same but the sequences included in the
packages are different.
Here is the description from the 1000 Genomes site:
http:
I'm curious what is this genome called 'hg_g1k_v37'
and how does it correspond to NCBI GRCh37 which is
identical to UCSC hg19 ?
--Hiram
Jennifer Jackson wrote:
UCSC does not contain the genome 'hg_g1k_v37' - the genome available
from UCSC is 'hg19'.
Even though these are technically the same
Hi Lilach,
The problem with this analysis probably has to do with a mismatch
between the genomes: the intervals obtained from UCSC (hg19) and the BAM
from your BWA (hg_g1k_v37) run.
UCSC does not contain the genome 'hg_g1k_v37' - the genome available
from UCSC is 'hg19'.
Even though these
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