mm39

[Jonathan Monin]

Is there  an IGB version including  GRCm39 ?

[Nowlan Freese]

The latest version of IGB (9.1.10) should include the GRCm39 (mm39) mouse genome version through the UCSC DAS data source by default.

To select the GRCm39 genome in IGB 9.1.10:

1. Select Mus musculus under the Species dropdown 
2. Then select M_musculus_Jun_2020 under the Genome Version dropdown.

Once the genome has loaded you will need to select which annotation to use:

1. In the Data Access tab, look at the left side to find the Available Data.
2. Click on the arrow next to UCSC (Das) to expand the annotation options.
3. Select your annotation of choice (I used ncbiRefSeqCurated).
4. Click Load Data to view the annotations for the current view in IGB, or to load that annotation's data across all chromosomes find the Data Management Table and select Genome under the Load Mode column.

If GRCm39 does not appear to be in IGB, it may be because the DAS data source has been disabled.

To enable the DAS data source:

1. In the Data Access tab, click on Configure
2. Look for the UCSC DAS Data Source.
3. Click the checkbox in the Enabled column to enable the UCSC DAS data source (there may be a slight pause/delay while the connection takes place).

Let me know if this helps!

Nowlan

[Jonathan Monin]

Thank you!

Enabling UCSC DAS did the trick.

[Stay with Rezanur & Tania]

Dear Nowlan

Thank you so much. I also had this issue and now resolved. I'll post some queries if I have about designing primers for my alternative splicing events.

Kind regards

Reza

The University of Queensland, Australia