12 Jul
2013
12 Jul
'13
8:12 a.m.
bedtools genomecov -bg -split -i stdin -g /usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/hg19.len
However this crashes. After looking in my computer, I find that bedtools do not contain the file genomecov. Is this an erroneous assumption of mine or have I installed something wrong?
genomecov is not a file, it is a parameter that indicates what operation to run. My guess is that you may have an old version of BEDtools installed; in this case, you'll need to update BEDtools. At minimum, BEDtools versions 2.15+ will work fine with Trackster/Galaxy. You can type this into your terminal to see the BEDtools version: bedtools --version Good luck, J.