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gene list for model evaluation #2
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Could you please provide the data for generating Fig.2? Jiecong |
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, |
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, |
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, |
By uncommenting the "write seqs" part here, you can generate the desired bed files. |
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
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