Running tutorials error about basenji

[davek44]

Hi Andy, that notebook isn't up to date for tensorflow2.*; sorry about that. I'll work on cleaning it up this week. In the meantime, you could try using the same command but replacing the parameters json and model file with those in this directory https://github.com/calico/basenji/tree/master/manuscripts/cross2020

[rpique]

Hi David. Andy got it to work at the end with the tf1 branch. Next, we would like to use predictions for lymphoblastoid cell-lines (LCLs) to compare chromatin QTLs and other annotations. We would prefer to avoid to train the model again, if possible, but in the tutorial model it seems that it is tailored to heart tissue. Do you have a model that is already trained for LCLs that we could use?

[davek44]

Yup, the model that I pointed you to above has many LCL-relevant datasets. You can see the full list here: https://github.com/calico/basenji/blob/master/manuscripts/cross2020/targets_human.txt

[davek44]

In case it's still beneficial to you, I just pushed an update to the tutorials.