custom BED to UCSC genome browser

Question

[npont]

Hi Biostars community,

I would like to display my methylation data on UCSC genome browser. I have a custom BED file as follows: column1 = chr, column 2 = start position of the motif bound by my methylase, column 3 = end position of motif, column 4 = methylation fraction for this motif, column 5 = number of methylated C in the motif, column 6 = number of unmethylated C in the motif, column 7 = total number of C matching the motif (can be superior to the number of C in the motif because it sum up the observations in the reads mapping the motif in the reference genome).

I am struggling to find how to display this on UCSC genome browser and which file format would be the best to use to upload my data as a custom track. Any help would be much appreciated!!

Thank you :)

Answer 1

[Maximilian Haeussler]

Hi, we just added bedMethyl support! Try it at https://genome-test.gi.ucsc.edu/cgi-bin/hgTables. type must be "bedMethyl". Please let us know if something doesn't work, we're looking for user feedback.

Answer 2

[barslmn]

BED files have specific format. https://genome.ucsc.edu/FAQ/FAQformat.html#format1 UCSC uses these columns to display the tracks. Your file might be a tab separated file, but it's not in BED format.

If you want to display tracks maybe you can make a color column based on the fraction. Or do you want to show number of methylated and unmethylated C's you might want to consider bedgraph format. It would be easier to answer your question if you can describe what you want to plot?

Answer 3

[npont]

Hello,

thanks for your replies. At the end, I created bedGraph files where each row contains the position of my methylation site and the fourth column is the methylation ratio. And therefore the methylation ratio is what is plot on the UCSC genome browser.

Thank you :)