Conversions between different genome versions

[PhrenoVermouth]

As we could see from the data hub, mm9 has much more epi-data than mm10. Isn't it possible to automatically convert mm9 to mm10 in datahub(e.g., using liftover)?

[caoxiaoyi03]

For now, there are several ways of changing references:

• Re-align everything in the new reference.
• Using liftOver on the raw reads and generate bigWig files again. Quality may not be as good and I'm not very sure if using liftOver for all reads has less computational burden than the previous one.

On the other hand, ENCODE is in the process of transiting from old reference genomes into the new ones (namely hg19 to hg38, and mm9 to mm10). We are discussing about how to synchronize with them (maybe in several stages or in one single batch once they are done).