Question about the scores in the input BED file

[Xunzhi Zhang]

Hello,

I want to input the sequences for motif discovery and enrichment by uploading a BED file with the coordinates and strand information. I wonder if the values in the 5th score column affect the results. May I set all the scores 0?

Thank you very much!

[cegrant]

All columns in a BED file are ignored except the chromosome name, start, end, and strand.

One thing to be cautious about is using a BED file that generates too much sequence data. If your BED file refers to more than 80 MB of sequence your job will be rejected. For motif discovery you'd typically want much less than 80MB.