BPNet manuscript data 1

This repository holds the trained BPNet models and all the output files produced using the models including TF-MoDISco files and motif instances.

Files:

output.tar.gz

Full output directory containing trained BPNet models, contribution scores, TF-MoDISco results, motif instances, etc.

See https://github.com/kundajelab/bpnet-manuscript for more information (archived at https://zenodo.org/record/4294814 with DOI: https://doi.org/10.5281/zenodo.4294813).

bpnet.model.h5

BPNet Keras model. This model can be directly used via the model repository Kipoi: http://kipoi.org/models/BPNet-OSKN . 

regions.bed

ChIP-nexus peak regions (resized to 1 kb width) where BPNet was trained and interpreted on.

Third column denotes the TF for which the peak was called.

motif-instances.bed

BPNet motif instances for 11 representative motifs

Stored as BED file with the following columns

Chromosome

Start

End

Motif name

'match' score - similarity to the CWM computed using the continuous Jaccard distance metric between the CWM and L1 normalized contribution scores

Strand

'contrib' score - computed as the L1 norm of the contribution scores at the motif instance position

The log odds score with respect to the PWM derived from the PFM (i.e. classical PWM score)

.preds..bw

Model predictions in `regions.bed` for a particular TF in {Oct4, Sox2, Nanog, Klf4} and strand in {pos, neg}.

.importance.counts.bw

Total count contribution scores for a particular TF

.importance.profile.bw

Profile contribution scores. These were used to run TF-MoDISco and downstream analysis.

PWM,CWM,ChIP-nexus-profiles.tar.gz

Directory containing PFM, CWM and aggregated ChIP-nexus footprint for 11 representative motifs.

Figure-5d-periodicity.csv

Raw data corresponding to Figure 5d where the 10bp periodicity of contribution scores was computed for each motif.

dfabf.Oct4-Sox2-subset.parq

Parquet file (read with `pd.read_parquet`) of genomics motif instance pairs and along with the BPNet-predicted interaction score.

See 08-motif-interactions.genomic.ipynb for more information on how to generate plots for Figure 5 from this data.