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?
2012/6/27 Lilach Friedman <lilac...@gmail.com>
> 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).
> 2012/6/26 Jennifer Jackson <j...@bx.psu.edu>
>> 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 convert data between different builds is not recommended.
>> These tools are very sensitive to exact inputs, which extends to naming
>> conventions, etc. The best practice path is to start and continue an
>> analysis project with the same exact genome build throughout.
>> If you want to use the hg19 indexes provided by the GATK project, a cloud
>> instance is the current option (using a hg19 genome as a 'custom genome'
>> will exceed the processing limits available on the public Galaxy instance).
>> Following the links on the GATK tools can provide more information about
>> sources, including links on the GATK web site which will note the exact
>> contents of the both of these genome versions, downloads, and other
>> Hopefully this helps to clear up any confusion,
>> Galaxy team
>> On 6/21/12 7:50 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 select), and I cannot
>> change it to hg19(full). Most probably, because I selected hg_g1k_v37 in
>> the previous time I tried to use DepthOfCoverage.
>> It seems as a bug? How can I change it?
>> 2012/6/18 Jennifer Jackson <j...@bx.psu.edu>
>>> 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 are technically the same human release, on a practical
>>> level, they have a different arrangement for some of the chromosomes. You
>>> can compare NBCI GRCh37<http://www.ncbi.nlm.nih.gov/genome/assembly/2758/>
>>> with UCSC hg19 <http://genome.ucsc.edu> for an explanation. Reference
>>> genomes must be *exact* in order to be used with tools - base for base.
>>> When they are exact, the identifier will be exact between Galaxy and the
>>> source (UCSC, Ensembl) or the full Build name will provide enough
>>> information to make a connection to NCBI or other.
>>> Sometimes genomes are similar enough that a dataset sourced from one can
>>> be used with another, if the database attribute is changed and the data
>>> from the regions that differ is removed. This may be possible in your case,
>>> only trying will let you know how difficult it actually is with your
>>> analysis. The GATK pipeline is very sensitive to exact inputs. You will
>>> need to be careful with genome database assignments, etc. Following the
>>> links on the tool forms to the GATK help pages can provide some more detail
>>> about expected inputs, if this is something that you are going to try.
>>> Good luck with the re-run!
>>> Galaxy team
>>> On 6/18/12 4:42 AM, Lilach Friedman wrote:
>>> I am trying to used Depth of Coverage to see the coverages is specific
>>> The intervals were taken from UCSC (exons of 2 genes), loaded to Galaxy
>>> and the file type was changed to intervals.
>>> I gave to Depth of Coverage two BAM files (resulted from BWA, selection
>>> of only raws with the Matching pattern: XT:A:U, and then SAM-to-BAM)
>>> and the intervals file (in advanced GATK options).
>>> The consensus genome is hg_g1k_v37.
>>> I got the following error message:
>>> An error occurred running this job: *Picked up _JAVA_OPTIONS:
>>> ##### ERROR
>>> ##### ERROR A USER ERROR has occurred (version 1.4-18-g80a4ce0):
>>> ##### ERROR The invalid argume
>>> *Is it a bug, or did I do anything wrong?
>>> I will be grateful for any help.
>>> 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:
>>> To manage your subscriptions to this and other Galaxy lists,
>>> please use the interface at:
>>> Jennifer Jacksonhttp://galaxyproject.org
>> Jennifer Jacksonhttp://galaxyproject.org
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:
To manage your subscriptions to this and other Galaxy lists,
please use the interface at: