Modification of mm9 genome

[Yasha Nazir Butt]

Hi Brian,I am trying to modify the C57BL6 mm9 reference genome specifically at chromosome 12 VDJ region to make it similar to CH12F3 reference genome that has a recombined (deleted parts as compared to C57BL6). Is there an easy quick way to modify (delete some region) of the reference genome so that it can be custom viewed on IGV?Best regards,Yasha

[Hiram Clawson]

Good Afternoon Yasha:

Can you clarify where the CH12F3 genome assembly can be obtained ?

--Hiram

[Brian Lee]

Dear Yasha,

When it comes to viewing the mm9 reference genome, we do have a tool called multi-region which allows one to drop a sequence region in your view. There is no underlying amending of the underlying genome, however, if you are looking at the mm9 reference genome at best you can only adjust the view.

For instance, if looking a chr12 for mm9 you could click the "multi-region" button on the left of the position box. Then you could enter your custom regions you wish to view. For instance, you could click the circular selection next to "Enter custom regions as BED, or a URL to them:" and then paste these regions.

chr12 114446755 114664845
chr12 114448382 114664909
chr12 114449569 114465003
chr12 114451347 114664909
chr12 114451353 114500280
chr12 114451782 114465259
chr12 114496057 114664909

You could also further select the box at the bottom "Highlight alternating regions in multi-region view" to help make it clear where one region ends and another region starts. The results would be a view like this one seen in this session, which also has a BLAT search of some sequence data.

Session link: http://genome.ucsc.edu/s/brianlee/Highlight_multi_region

Thank you again for your inquiry and for using the UCSC Genome Browser. If you have any further public questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,