Hello,
I’m trying to reproduce Chrombpnet becnhmark from Extended Data Fig 3g and having trouble achieving the reported correlation with Chrombpnet.
My command:
chrombpnet pred_bw -cm chrombpnet_model.h5 -r bed10.bed -g hg38.fa -c hg38.chrom.sizes -op DNASE/GM12878 -bw ENCFF681PTG.bigWig
The model and the bigwig files were downloaded from ENCSR003WJE – ENCODE (the model was reformatted using reformat_chrombpnet_h5.py). I wanted to use bed3 file for the regions (which is just chrombnet fold_0 testing regions with Alpha genome training regions excluded). So I tried to reformat it to bed10, according to the F.A.Q.: the resulting file gives me “RuntimeError: Invalid interval bounds!”, unless I exclude the regions in the beginning of the chromosomes. then I get some result, but the correlation is not the same as reported in the article.
I understand it may be the wrong place for Chrombnet questions, but I’m a little desperate. Perhaps you could share the code/logic you used for Chrombpnet becnhmark from Extended Data Fig 3g?
Thanks,
Galina