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zhongzhd / ont_m6a_detection

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Coordinate transformation issue #5

Closed SEVEN-XYCHEN closed 1 year ago

SEVEN-XYCHEN commented 1 year ago

Hello， The result obtained by the MINES software is the location coordinate of the Transcriptome. How should I convert it into the location coordinate of the corresponding genome? That is to say, how to obtain the bed file below？

1687701382336(1) Best, Chen

kwonej0617 commented 1 year ago

@SEVEN-XYCHEN

I reached out to the author for this issue. He said because he was not able to log in the GitHub for some reason, I am sharing what I got from the author as follows.

" Regarding the issue itself, you can use metaPlotR (https://github.com/olarerin/metaPlotR) to get the bed file you want. You can use make_annot_bed.pl from metaPlotR creates a master annotation file (bed format) of every nucleotide in the transcriptome similar to the picture below, then you can easily convert it into the "bed=path_to_genome_transcriptome_coordinate" with awk tools."

image

SEVEN-XYCHEN commented 1 year ago

Thank you very much for your help! Best, Chen