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WGLab / DeepMod

DeepMod: a deep-learning tool for genomic-scale, strand-sensitive and single-nucleotide based detection of DNA modifications
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What are 7th-9th columns in the output? #40

Closed PanZiwei closed 3 years ago

PanZiwei commented 3 years ago

Hi, I checked the result explanation for the output file, but I still have questions on the column meanings. Can you tell more about the 7th-9th columns(148655 148656 0,0,0) especially the 9th column?

Thank you so much for your help!

liuqianhn commented 3 years ago

@PanZiwei I think you can ignore these columns for now and column 9 is not meaningful, since I tried to make the output compatible with BED format using them. Sorry for the confusion.

PanZiwei commented 3 years ago

Hi @liuqianhn , Thank you so much for the quick response. I have one more question on the 8th column Methylation percentage in the output file. Does methylation percentage show the methylation frequencies at the CpG site? Is it measured at the genome level or per-read level?

Thanks!

liuqianhn commented 3 years ago

@PanZiwei Methylation percentage is not in the 8th column but in the last second column. The percentage is for a C at a CpG site, and thus it summarizes all methylations of all long reads whose bases are aligned against this site: it is calculated by the number of methylation prediction at this site divided by the total number of reads aligned against this site. Per-read level prediction is in intermediate files.