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10.3 years ago
Hi, I am new and so facing problem. I was trying to make a bed graph file using bed tools genomecov command. The command was: bedtools genomecov -ibam filename.sorted.bam -g chromosome sizes.txt > O.bedgraph I got a bedgraph file which is much smaller in size. It is 500kb instead of ~6Mb. And when I load that 500kb file into IGV, I see nothing. Please help me out.
Try zooming in, it may not show up at your current zoom level. BTW, if you just load the BAM file then IGV will show the coverage anyway.
The default behavior is to report a histogram. Use the -bg option for a BEDGRAPH. Docs: http://bedtools.readthedocs.org/en/latest/content/tools/genomecov.html#bg-reporting-genome-coverage-in-bedgraph-format