documentation on how to load hg38 dataset to the database #6847
Conversation
khzhu
force-pushed
the
doc-on-multiple-ref-genomes-6729
branch
from
1e2dd2a
to
38686d6
Compare
There was a problem hiding this comment.
@khzhu instead of creating a new file, I am wondering if we should add the text to the existing files, eg. https://docs.cbioportal.org/5.1-data-loading/data-loading/file-formats#cancer-study?
| @@ -0,0 +1,35 @@ | |||
| # [Introduction](introduction) | |||
| From release 3.1, cBioportal supports multiple reference genomes. This means the hg19 datasets can co-exist with the hg38 ones in the same portal database. We also support mouse genomes (mm10), but it is not recommended to have both human and mouse data in the same instance of the cBioPortal. | |||
There was a problem hiding this comment.
@khzhu I make some change here. I change the version from 2.2 to 3.1. Was 2.2 referred to the db version? I think the portal code version should be used.
I also change the text about mouse genome and recommend not to import human and mouse into the same instance.
There was a problem hiding this comment.
thanks, @jjgao, for the review! merged with your changes.
| 1. [Import Reference Genome](Import-reference-genome) into your cBioPortal database. If the version of your portal instance is lower than 3.1, you will have to [update your cBioPortal installation](Updating-your-cBioPortal-installation) | ||
| and migrate your database schema to the latest. The migrartion script by default will add three reference genomes (hg19, hg38, mm10) to the database. | ||
| 2. [Update the reference genome gene database table](Updating-gene-and-gene_alias-tables) to include the genes from the reference genome of interest to the database. You will also need to update both gene and gene alias tables in order to support other species such as mouse. |
There was a problem hiding this comment.
If I start a new instance from scatch, do I need # 1&2 or are they included in the seed db?
If I migrate my db, will the migration script take care of both 1&2?
There was a problem hiding this comment.
if you are using a seed database to restore you database or using the migration script you will still need to do step 2 to add genes from your new reference genome.
| * You can also overwrite default genome values by using the following options of the importer script: | ||
| ``` | ||
| -species SPECIES, --species SPECIES | ||
| species information (default: assumed human) | ||
| -ucsc UCSC_BUILD_NAME, --ucsc_build_name UCSC_BUILD_NAME | ||
| UCSC reference genome assembly name (default: assumed | ||
| hg19) | ||
| -ncbi NCBI_BUILD_NUMBER, --ncbi_build_number NCBI_BUILD_NUMBER | ||
| NCBI reference genome build number (default: assumed | ||
| GRCh37 for UCSC reference genome build hg19) | ||
| ``` | ||
| The **species** by default is human. You do not need to supply it unless you try to add datasets from other species such as a mouse. **ucsc** and **ncbi** are both required | ||
| when loading hg38 datasets into the portal database. For instance, to load hg38 dataset: | ||
| ``` | ||
| core/src/main/scripts/importer/metaImport.py -s /path/to/your/study -jar scripts.jar -ucsc hg38 -ncbi GRCh38 -n -o | ||
|
|
||
| ``` |
There was a problem hiding this comment.
Maybe remove this for simplicity so that people alway change their meta file?
There was a problem hiding this comment.
meta file is only used for populating the cancer_study table.
the validation script uses ucsc/ncbi options to validate the reference genome when importing any studies profiled with a different genome other than a default genome value listed in portal properties file.
also, those default genome values are used by the importer script (java script) if no ucsc/ncbi values supplied by the user.
…w comments from JJ
khzhu
force-pushed
the
doc-on-multiple-ref-genomes-6729
branch
from
a4ecfd7
to
931b6d2
Compare
|
Hi @jjgao , I've resolved all of your comments. May I please have your approval to get documentation merged or let me know if anything else need to be done. Thanks! |
Fix #6729
Describe changes proposed in this pull request:
Checks
Any screenshots or GIFs?
If this is a new visual feature please add a before/after screenshot or gif
here with e.g. GifGrabber.
Notify reviewers
Read our Pull request merging
policy. It can help to figure out who worked on the
file before you. Please use
git blame <filename>to determine thatand notify them either through slack or by assigning them as a reviewer on the PR