bedgraphToBigWig error

Question

[Mireia]

Hello,

I would like to transform a BedGraph file into a BigWig file using R. For this purpose I run the next code:

Bedgraph <- import_bedGraph('//nasibv05/datos/Grupos/UGC/RROxBS/KO1_BS/KO1_BS.bedGraph')

bedgraphToBigWig(Bedgraph, genomeSizeFile = "//nasibv05/datos/Grupos/UGC/RROxBS/KO1_BS/KO1_BS.bedGraph", ucscPath = "/opt/UCSCtools/",
                 outDest = "//nasibv05/datos/Grupos/UGC/RROxBS/KO1_BS/", outSuffix = "KO1_BS.bigwig")

And I get this error:

Error in dir_check(ucscPath) : Directory /opt/UCSCtools/ does not exist.

I would like to know what I need to write into the ucscPath argument in order to make the function work properly.

Thank you!

[Arup Ghosh]

Make sure you have UCSCtools available in the mentioned location. If you are using E-myers/rnaseq , the bedgraphToBigWig function is a wrapper of the bedGraphToBigWig binary. Also, the genomeSizeFile parameter expects a text file containing the genome size information.