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Output format
Anusri Pampari edited this page Dec 29, 2022
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Here is a detailed description of all the files generated as a part of ChromBPNet model training
models\
bias_model_scaled.h5
This is the final bias model in use for bias correction and is different from the input bias model by a scaling
factor on the counts head. The scaling factor accounts for the difference in read-depths of the bias model training dataset and
the current observed dataset
chrombpnet.h5
This is the bias factorized chromBPNet model that trains on the observed accessibility. This model is the combination of
bias_model_scaled.h5 and chrombpnet_nobias.h5
chrombpnet_nobias.h5
TF-Model i.e model to predict bias corrected accessibility profile
logs\
chrombpnet.log
Train and validation loss per epoch
chrombpnet.log.batch
Train loss per batch per epoch
chrombpnet.args.json
Arguments used in training the chromBPNet model
chrombpnet_data_params.tsv
Stats on training data regions
chrombpnet_model_params.tsv
Model parameters used in training
auxiliary\
filtered.peaks.bed
Final peak regions used in training in bed format
filtered.nonpeaks.bed
Final non peak regions used in training in bed format
data_unstranded.bw
Bigwigs with observed accessibility profiles used as ground truth in training
motif_to_pwm.tsv
Bias motifs used in getting marginal footprints
chrombpnet_nobias_footprints.h5
Marginal footprints on bias motifs
30K_subsample_peaks.bed
30K peaks subsampled for interpretation and TFModisco. See [FAQ](https://github.com/kundajelab/chrombpnet/wiki/FAQ) on why we
subsample peaks
interpret_subsample/chrombpnet_nobias.interpreted_regions.bed
30K peaks subsampled for interpretation and TFModisco. This is same as 30K_subsample_peaks.bed
interpret_subsample/chrombpnet_nobias.profile_scores.h5
Profile contribution scores on each of the 30K subsampled peak regions
interpret_subsample/modisco_results_profile_scores.h5
TFModisco lite object output generated from interpret_subsample/chrombpnet_nobias.profile_scores.h5
interpret_subsample/chrombpnet_nobias.interpret.args.json
Arguments used in running the interpretation script
evaluation\
overall_report.pdf
This is a pdf summary report of most of the remaining outputs in this folder. It also has guidelines on how to
interpret the results
overall_report.html
This is a html summary report of most of the remaining outputs in this folder. It also has guidelines on how to
interpret the results
bw_shift_qc.png
This image should show the enzyme bias motif and is generated from the final shifted bigwigs. If this shows the bias motif it
indicates that the bams are correctly shifted.
epoch_loss.png
Bias factorized ChromBPNet training and validation loss change with epoch
bias_predictions.h5
Bias model predictions on peak regions
bias_metrics.json
Bias model metrics on peak regions
bias_only_peaks.counts_pearsonr.png
Scatter plot of observed and bias model predicted log counts on peak regions
bias_only_peaks.profile_jsd.png
Histogram of pairwise JSD calculated between observed and predicted bias model profiles on peak regions overlayed with
histogram of pairwise JSD calculated between observed and randomized profiles for worst case
chrombpnet_predictions.h5
Bias factorized ChromBPNet model predictions on peak regions
chrombpnet_metrics.json
Bias factorized ChromBPNet model predictions on peak regions
chrombpnet_only_peaks.counts_pearsonr.png
Scatter plot of observed and Bias factorized ChromBPNet model predicted log counts on peak regions
chrombpnet_only_peaks.profile_jsd.png
Histogram of pairwise JSD calculated between observed and predicted Bias factorized ChromBPNet model profiles on peak regions
overlayed with histogram of pairwise JSD calculated between observed and randomized profiles for worst case
chrombpnet_nobias.....footprint.png
Marginal footprint profiles of chrombpnet_nobias.h5 on the bias motifs (name tn5_1, tn5_2.. tn5_5 for ATAC and dnase_1, dnase_2
for DNase)
chrombpnet_nobias_max_bias_response.txt
Mean of Max of the marginal footprint profiles of chrombpnet_nobias.h5 on the bias motifs and individual max on each of the
profiles (name tn5_1, tn5_2.. tn5_5 for ATAC and dnase_1, dnase_2 for DNase)
chrombpnet_nobias_profile_motifs.pdf
TFModisco motifs obtained from the contribution scores of chrombpnet_nobias.h5 profile head in pdf format
modisco_profile/motifs.html
TFModisco motifs obtained from the contribution scores of chrombpnet_nobias.h5 profile head in html format
Here is a detailed description of all the files generated as a part of bias model training
models\
bias.h5
This is the bias model that trains on the observed accessibility in non peak regions.
logs\
bias.log
Train and validation loss per epoch
bias.log.batch
Train loss per batch per epoch
bias.args.json
Arguments used in training the chromBPNet model
bias_data_params.tsv
Stats on training data regions
bias_model_params.tsv
Model parameters used in training
auxiliary\
filtered.nonpeaks.bed
Final non peak regions used in training in bed format
data_unstranded.bw
Bigwigs with observed accessibility profiles used as ground truth in training
30K_subsample_peaks.bed
30K peaks subsampled for interpretation and TFModisco. See [FAQ](https://github.com/kundajelab/chrombpnet/wiki/FAQ) on why we
subsample peaks
interpret_subsample/bias.interpreted_regions.bed
30K peaks subsampled for interpretation and TFModisco. This is same as 30K_subsample_peaks.bed
interpret_subsample/bias.profile_scores.h5
Profile contribution scores on each of the 30K subsampled peak regions
interpret_subsample/modisco_results_profile_scores.h5
TFModisco lite object output generated from interpret_subsample/chrombpnet_nobias.profile_scores.h5
interpret_subsample/bias.counts_scores.h5
Counts contribution scores on each of the 30K subsampled peak regions
interpret_subsample/modisco_results_counts_scores.h5
TFModisco lite object output generated from interpret_subsample/chrombpnet_nobias.counts_scores.h5
interpret_subsample/chrombpnet_nobias.interpret.args.json
Arguments used in running the interpretation script
evaluation\
overall_report.pdf
This is a pdf summary report of most of the remaining outputs in this folder. It also has guidelines on how to
interpret the results
overall_report.html
This is a html summary report of most of the remaining outputs in this folder. It also has guidelines on how to
interpret the results
bw_shift_qc.png
This image should show the enzyme bias motif and is generated from the final shifted bigwigs. If this shows the bias motif it
indicates that the bams are correctly shifted.
epoch_loss.png
Bias model training and validation loss change with epoch
bias_predictions.h5
Bias model predictions on peak and non peak regions
bias_metrics.json
Bias model metrics on peak and non peak regions
bias_only_peaks.counts_pearsonr.png
Scatter plot of observed and bias model predicted log counts on peak regions
bias_only_peaks.profile_jsd.png
Histogram of pairwise JSD calculated between observed and predicted bias model profiles on peak regions overlayed with
histogram of pairwise JSD calculated between observed and randomized profiles for worst case
bias_only_nonpeaks.counts_pearsonr.png
Scatter plot of observed and bias model predicted log counts on non peak regions
bias_only_nonpeaks.profile_jsd.png
Histogram of pairwise JSD calculated between observed and predicted bias model profiles on non peak regions overlayed with
histogram of pairwise JSD calculated between observed and randomized profiles for worst case
bias_profile_motifs.pdf
TFModisco motifs obtained from the contribution scores of bias.h5 profile head in pdf format
modisco_profile/motifs.html
TFModisco motifs obtained from the contribution scores of bias.h5 profile head in html format
bias_counts_motifs.pdf
TFModisco motifs obtained from the contribution scores of bias.h5 counts head in pdf format
modisco_counts/motifs.html
TFModisco motifs obtained from the contribution scores of bias.h5 counts head in html format