gene list for model evaluation

[JasonLinjc]

Dear All,

I'm trying to compare our model with graphReg, could you please provide the gene list and the true CAGE signal of each gene for 10-fold cross-validation (hold two chromosomes out)?

Best Regards,
Jiecong

[JasonLinjc]

Could you please provide the data for generating Fig.2?

Jiecong

[karbalayghareh]

Hi Jiecong,

All data (including CAGE) can be downloaded from ENCODE portal and their accession numbers are provided in data set section of the paper (https://genome.cshlp.org/content/32/5/930.full.pdf+html). After you downloaded the raw data, follow step-by-step tutorial (https://github.com/karbalayghareh/GraphReg/blob/master/README.md) to preprocess the data. Then you will have all the required data for training the models.

Best,
Alireza

[JasonLinjc]

Hi Alireza,

Thanks for your reply!

I'm trying to reproduce your model following your tutorial. For running find_TSS.py, could you please provide the file of the script to generate the bin bed? (i.e., filename_seqs = data_path+'/data/csv/seqs_bed/'+organism+'/'+genome+'/'+resolution+'/sequences_'+chr+'.bed')

Thanks,
Jiecong

[JasonLinjc]

Hi Alireza,

Would it be possible to have the table for generating Fig.2 in the paper? For example, "gene_name, predicted_CAGE, actual_CAGE"?

Thanks,
Jiecong

[karbalayghareh]

By uncommenting the "write seqs" part here, you can generate the desired bed files.