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
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> 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: