rmsk fetch error - Githubissues

Hi,

Followed the CNEr workflow outlined in https://bioconductor.org/packages/release/bioc/vignettes/CNEr/inst/doc/CNEr.html#cne-identification.

At least for me it seems the rmsk-fetch step fails using the following code: mySession <- browserSession("UCSC") genome(mySession) <- "hg38" hg38.rmsk <- getTable(ucscTableQuery(mySession, track="RepeatMasker", table="rmsk")) `hg38.rmskGRanges <- GRanges(seqnames=hg38.rmsk$genoName,

The UCSC coordinate is 0-based.

                        ranges=IRanges(start=hg38.rmsk$genoStart+1,
                                       end=hg38.rmsk$genoEnd),
                        strand=hg38.rmsk$strand)`

Manual download from UCSC gives ~5+M-lines of elements but download using code above only fetches 1M lines. Don't know if there is some extra option one can use to get the full matrix but on my machine I get 1M lines. Ran your excellent pipeline some years back and then I got the full rmsk-file. Rerunning same code now does not.

ge11232002 / CNEr

rmsk fetch error #25

The UCSC coordinate is 0-based.