Question: Homo_sapiens_nuHg19_mtrCRS vs hg_g1k_v37
0
gravatar for srinivasn.kumar
3.1 years ago by
United States
srinivasn.kumar0 wrote:

What is the difference between Homo_sapiens_nuHg19_mtrCRS vs hg_g1k_v37. I used bra-mem to align sequence to Homo sapiens b37 hg19. The output does not show this the 'database' field in the History column. It instead shows a '?'. Upon clicking this I can only assign the database to either Homo_sapiens_nuHg19_mtrCRS or hg_g1k_v37 but not what I previously chose during the alignment (b37 hg19). I am a little confused as to why this occurred and why it failed to detect the reference sequence post alignment automatically. Thanks

 

 

 

 

 

 

bwa alignment • 970 views
ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by srinivasn.kumar0
0
gravatar for Jennifer Hillman Jackson
3.1 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Homo_sapiens_nuHg19_mtrCRS is a composite reference genome we created that contains all the same data as hg19 except that the mitochondrial genome was swapped out with the updated Cambridge release. hg19 uses the mito release present in earlier human genome releases (hg17, hg18). hg_g1k_v37 uses the updated mito release. All three are different with respect to either chromosome identifiers or sequence content and should not be intermixed in an analysis. 

If you have an example of a BWA-MEM job that was run with a built-in index (like hg19) at http://usegalaxy,org and the database metadata attribute was not assigned, please submit a bug report so that we can review the root cause. Please leave all inputs and outputs undeleted and include a link to this post in the comments. 

If the job was run elsewhere, there could be other issues. Checking to see if this is reproducible at http://usegalaxy.org is one way to test if what job configuration issues could be present alternate server. Or if this is your own local/cloud, double check that you are running the latest version of the tool wrapper (with managed installed dependencies) and have indexed the genome(s) using Data Manager tools.

Hopefully this leads to a solution, but we will watch for the bug report is one is sent in. Jen, Galaxy team 

ADD COMMENTlink written 3.1 years ago by Jennifer Hillman Jackson25k
0
gravatar for srinivasn.kumar
3.1 years ago by
United States
srinivasn.kumar0 wrote:

Thanks Jen. I decided to rerun bwa-mem using hg_g1k_v37 as reference and assigning this reference for all subsequent steps of file manipulations. Reassigning the 'Database' field each time to hg_g1k_v37 has not proved to be an serious impediment for subsequent manipulation (e.g., using the latest version of GATK in command line format) but was somewhat surprising. 

ADD COMMENTlink written 3.1 years ago by srinivasn.kumar0
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