how to use bedmethyl tobigwig..?

[Seongmin-Jang-1165]

Hello developer!!

I tried to use bedmethyl tobigwig function for m6A site visualization in IGV, but I don't know the proper input file and information.

the input bedmethyl file is generated by modkit pileup without any option(the end of filename is .bed), and use gencode.v43.transcripts.fa.fai for --sizes option.

but It didn't work. what file should I use for bedmethyl tobigwig??

the one thing is that I generated the bedmethyl file with older version, so the transcript/gene decription(gene ID information) is tab-separted.

Code
modkit bedmethyl tobigwig --sizes gencode.v43.transcripts.fa.fai --mod-codes a --negative-strand-values --nthreads 10 --log-filepath modkit/output/modkit_bigwig/B2_log modkit/output/m6A_barcode2.bed modkit/output/modkit_bigwig/B2_bigwig

[KunFang93]

Not developer but these code works for me

modkit bedmethyl tobigwig foo.bedmethyl --mod-codes h -t 40 -g sizes.genome foo.bigWig

where sizes.genome something like

chr1    248956422
chr2    242193529
chr3    198295559
chr4    190214555
chr5    181538259
chr6    170805979