bm2-lab / deepcrispr Goto Github PK

I'm wondering how we're supposed to encode epigenetic information for passing into the "off-target" version of the pipeline. The model wants both the sgRNA and the target as 8-channel vectors that include epigenetetic information ... what should we put in those channels on the sgRNA? Should they be zeros? Should they match what is in the target?

I'm trying to run the off-target scoring algorithm and I'm not getting any values that make sense. Even perfect matches between the sgRNA and the target are giving extremely low values.

off_target_model_dir = '../DeepCRISPR/trained_models/offtar_pt_cnn/'
is_reg = False
dcmodel_off = DCModelOfftar(sess, off_target_model_dir, is_reg)
seq = 'GTTAGACCAGATCTGAGCCTTGG'
encoded = encoder([seq]) #Does one-hot encoding to correct shape, all epigenetic factors are zero
res = dcmodel_off.offtar_predict(encoded, encoded)
# res = 1.4075727e-35

I've tried all combinations of epi factors and the scores are still very low. Since the sgRNA and target are exact matches I would expect a 100% score, or at least something reasonably high for at least one combination of epi factors.

Am I encoding things wrong? Am I misunderstanding your paper and it is actually low values that are indicative of off-target activity?

I've run this across a large collection of sgRNAs across various targets to compare this with the CFD score.

Here I've plotted the maximum DeepCRISPR score across all of the different epi-conditions for each sgRNA/target pair vs the CFD score for the same pair. No DeepCRISPR score is above 1E-7 Something is clearly going wrong.

Can you help me understand what I'm doing wrong here. I am able to get sensible results out of these sgRNAs out of the on-target pipeline.

Hi, Can you add (DCDNN)-based autoencoder standalone model with an example input and output?

nonetype object has no attribute ‘model_checkpoint_path’

dm-sonnet version == 1.9 does not exist - which version is compatible with the current code?
//
says 1.9 but 1.19 works

Hi, the data for evaluation g) (Testing scenario 8—regression schema on an independent dataset) of the paper is not in the data zip, can you provide this data both for classification and regression.
thank you

I'm getting this error while running run_examples.py :

I've tried Python versions 3.6.9, 3.6.0, Tensorflow 1.3.0 and dm-sonnet 1.19.
I am not sure how to fix this issue. Any help would be appreciated.