For annotation of Differentially methylated regions using genomation package. I require bed12 file. For that I used MSU rice gff3 file and converted it to bed format using bedtools. When I am putiing this file in the readtranscriptfeature command.
It shows "Error in rep(1:nrow(ref, ref[,10]): invalid 'times' argument. And warning message: NAs introduced by coercion.
Hi, I guess from the error message that your bed file doesn't have a 10th column that is required for the `readTranscriptFeatures` function, which means that your bed file is not in the bed12 format. Mabe check out arguments of a bedtools function that you used so that it converts your gff file to bed12 format or use another tool. Usually, you might get a faster response if you post your issue on github issues page of genomation (https://github.com/BIMSBbioinfo/genomation) or methylKit (https://github.com/al2na/methylKit/issues)
Cheers, Kasia
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