GIGGLE score = 0 for large single base interval BED file

[June Tan]

Hi Ryan,

We are researching on some potential functional SNPs and are wondering if they are overlapping with any TF, histone modification or chromatin accessibility datasets. We plan to convert the these candidate SNP centered loci as a BED file (as a peak set) to do GIGGLE score analysis, while prepare another whole genome scale SNP BED file as a reference. All BED file are most with same start and end coordinates. We found when the BED file contains over 1000 lines, the GIGGLE tends to give ALL zero GIGGLE score (when the lines less than 500, the results are fine). Can you help on this?

June

[Ryan Layer]

Sure. Do you have a file you can share?

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