After running MINES with HEK293T data, I compared my result with your result, which was generated by running MINES with supplementary files in NCBI GEO (HEK293_WT_genomic.coverage.minus/plus.bedagraph.gz and HEK293T_WT.Genomic.fraction_modified_reads.minus/plus.wig.gz).
Here's a comparison result.
Blue (#9507): location of m6a sites, fraction modified, coverages are identical to your data.
Brown (#5102): location of m6a sites is identical to your data, but fraction modified and coverages are different.
Pink (#2828): the number of m6a sites found in your data but not in my data.
Green (#2184): the number of m6a sites found in my data but not in your data.
Although many sites in my data are overlapped with your data, more than 10% of sites in your data are not found in my data. I followed the same command lines you suggested in the github, so I assume the different guppy version could make a different result and may impact the result. Could you please tell me which version of guppy you used to process the supplementary files in NCBI GEO.
Hi, Thank you for making the useful tool.
After running MINES with HEK293T data, I compared my result with your result, which was generated by running MINES with supplementary files in NCBI GEO (HEK293_WT_genomic.coverage.minus/plus.bedagraph.gz and HEK293T_WT.Genomic.fraction_modified_reads.minus/plus.wig.gz). Here's a comparison result.
Blue (#9507): location of m6a sites, fraction modified, coverages are identical to your data.
Brown (#5102): location of m6a sites is identical to your data, but fraction modified and coverages are different.
Pink (#2828): the number of m6a sites found in your data but not in my data.
Green (#2184): the number of m6a sites found in my data but not in your data.
Although many sites in my data are overlapped with your data, more than 10% of sites in your data are not found in my data. I followed the same command lines you suggested in the github, so I assume the different guppy version could make a different result and may impact the result. Could you please tell me which version of guppy you used to process the supplementary files in NCBI GEO.
Thank you for your help!