kimmo1019/deepcage

Incorporating Transcription Factors in Genome-wide Prediction of Chromatin Accessibility

deepcage's Issues

How to apply DeepCAGE into my own dataset?

Hi,

Thanks for DeepCAGE software. I would like to apply this model to my custom data which contains RNA expression (TPM) values for different cell types. Could you let me know, how to prepare the input files to run "python 5.Regression.py <GPU_ID> <FOLD_ID>"

Minimum example files to run 4.classification and 5.regression

Dear author,
Thanks for providing the very useful software. I wish to run classification and regression using my own custom data but it seems that the manual page does not give sufficient information as the exact data format (e.g. whether it's tab or comma delimited, whether the genomic location information should be provided in any file, how I should prepare five_fold_cells.txt, etc). I wonder whether it would be possible to provide a minimum set of example input files for 4.classification and 5.regression so I can prepare my own files accordingly?
Thanks a lot in advance!

missing geneid2name.txt and whole_genome_200bp.bed

Hi,

the release is missing some files : geneid2name.txt and whole_genome_200bp.bed

While I could modify the code and use gencodeV19.gtf and create a whole_genome_200bp.bed, it would be nice if you could add these files for download.

Thanks