Chrombpnet model uncorrected

[linzyzhao2002]

Hello,

Hope this message finds you well. I am encountering a problem during training the chrombpnet model, where the report says "the model is uncorrected, average of the max of the profiles is 0.024". However, based on the Tn5 profile below, the maximum is below 0.001.

Additionally, I am training using a pretrained bias model, using the same peak and non-peak regions as the chrombpnet model. Please let me know why the error occurs, and any help would be deeply appreciated!

[panushri25]

Can you share your full report?

[panushri25]

Also if you can share the full output directory that will be helpful

[linzyzhao2002]

Can you share your full report?

Thank you so much for your help!! This is the output for my chrombpnet model:
train model output 19.pdf

This is the model output for my bias model:
bias model output.pdf
I trained the bias model with hyper parameter of 0.4.

[linzyzhao2002]

Also if you can share the full output directory that will be helpful
slurm_54367172.pdf
I'm attaching the full output directory.

Any help would be greatly appreciated - thank you so much for your time and help!!!

[linzyzhao2002]

Also just to add, I noticed that the pearsonr in peaks is always >0 (around 0.30) for the bias model. Could this be the problem here? Does this suggest anything wrong with the peak file or the bam file?

I generated the peak file using macs2 callpeak with qvalue cutoff of 0.01 and then removed the blacklist region. The bam files i used was deduplicated/removed MT reads. Please let me know and thank you so much for your help!!

[panushri25]

@linzyzhao2002 noticed you posted on the other thread too. Are you merging peaks across celltypes as well?

[linzyzhao2002]

@linzyzhao2002 noticed you posted on the other thread too. Are you merging peaks across celltypes as well?

No I'm not. I am training chrombpnet on only one cell type (bulk ATAC-seq for mouse T cells), sampled at different time points (0h, 2h, 5h etc). My bias model was trained with peaks called at the 5h time point. Do you have any suggestions? Thank you so much!

[linzyzhao2002]

Adding to the context, I am doing analysis on time-course ATAC-seq for in vitro activated mouse T cells. I am using a single time-point (say 5h) for training the bias model. I then use this bias model to train my chrombpnet model on the 5h timepoint bam file. However, I observed that the nobias model was uncorrected (average profile maximum for Tn5 is 0.024), and that Tn5 motifs were observed by TFmodisco. I tried sweeping the hyper-parameter (from 0.2 to 0.5) but still got the same results. Could you please let me know what could be happening here? Thank you so much!!

Sincerely,
Linzy