Example for seq, labels & chromatin track

[tuannguyen8390]

Hi there,

I wonder if you can provide a small example in the current repo to run your program ? To be precise, I am unsure of the formatting of labels & chromatin_tracks

train:  
  seq: '/path/to/train/seq.txt'    
  labels: '/path/to/train/labels.txt'  
  chromatin_tracks: ['/path/to/train/atacseq.txt', ..., '/path/to/train/h3k27ac.txt']  

val: 
  seq: '/path/to/val/seq.txt'  
  labels: '/path/to/val/labels.txt'  
  chromatin_tracks: ['/path/to/val/atacseq.txt', ..., '/path/to/val/h3k27ac.txt'] 

test: 
  seq: '/path/to/test/seq.txt'  
  labels: '/path/to/test/labels.txt'  
  chromatin_tracks: ['/path/to/val/atacseq.txt', ..., '/path/to/test/h3k27ac.txt'] 

Best,

Tuan Nguyen

[DivyanshiSrivastava]

Hi Tuan,

Thanks for raising this issue - we have added in sample files.

However, we realize that these input formats decrease usability and are not required for standard usage. We have therefore added in functionality to automatically generate the sequence, labels and chromatin track files. To make the program more usable, we have redefined inputs to be the fasta files of interest, peak files and chromatin bigWig files. Please let us know if this makes things better. I will continue to test this for a couple of days, and close this issue if this works well.

Thanks, Divyanshi

[yztxwd]

Closed due to no activity