modkit bm tobigwig

[gsukrit]

Hello @ArtRand ,

I am trying to use my modkit pileup output for visualization in IGV. When I am directly trying to open the bedmethyl file in IGV, I get the following error:

The bed file looks like this:

When I am using the command

home/modkit bm tobigwig PF_CpGpileup.bed.gz PF_CpG.bw --mod-code m -g media/RESEARCH_DATA/SUKRITI/PlasmoDB64_Pfalciparum3D7_Genome.fasta.fai - --negative-strand-values

I am getting an error like:

loaded 16 chromosomes
Error! stream did not contain valid UTF-8

The first few lines of the .bed.gz file reads:

I am using the .fai of reference fasta for -g argument

When I use the following command, I am getting an error as pasted below:
(base) administrator@administrator-Precision:/media/RESEARCH_DATA/SUKRITI/R10/modkitv0.6.1_R10/AllContextBasecall/CGpileup/bigwigfiles$ tabix PF_CpGpileup.bed.gz $chrom:$start-$end | /home/administrator/modkitv0.6.1/dist_modkit_v0.6.1_481e3c9/modkit bedmethyl tobigwig - PF_5mC_CpG.bw -g /media/RESEARCH_DATA/SUKRITI/PlasmoDB64_Pfalciparum3D7_Genome.fasta.fai --mod-codes m

loaded 16 chromosomes
Error! no bedmethyl lines

Could you please guide as to what might be wrong here.

Thank you for your continued support.

Sukriti