Hello, In an earlier thread: BED to WIG format conversion (Thu 9/17/2009 4:50 PM) Michael Lawrence mentioned:
Ignoring efficiency, it's pretty straight-forward. In the development version of IRanges, one can convert an Rle (or RleList for multiple chromosomes) as output to coverage() to a RangedData. In the development version of rtracklayer, this is done implicitly: > export(cov, "coverage.wig") as a way to create a wig file from a coverage() result. When I try this, my wig file looks like the following: track name="R Track" type=wiggle_0 . 0 2 168 . 2 4 175 . 4 5 177 . 5 7 178 . 7 8 182 . 8 12 185 . 12 14 188 . 14 15 191 etc. This isn't compatible with any of the UCSC wig formats that I'm aware of (is it?). Shouldn't rtracklayer be putting out a variableStep format for this? Am I doing something wrong? By the way, here is my work flow for going from solexa export to coverage: # read in some IP data aln <- readAligned(spath, pattern="s_1_export.txt", type="SolexaExport", filter=filt) # convert to GenomeData object s1 <- as(aln,"GenomeData") # read in some WCE data aln <- readAligned(spath, pattern="s_3_export.txt", type="SolexaExport", filter=filt) # convert to GenomeData object s3 <- as(aln,"GenomeData") # create GenomeDataList from ip and wce ypd <- GenomeDataList(list(ip=s1, wce=s3)) # extend reads ip1 <- extendReads(ypd$ip$chrI, seqLen=150) wce1 <- extendReads(ypd$wce$chrI, seqLen=150) # find coverage for chromosome 1 ip1.cov <- coverage(ip1, width=230208) wce1.cov <- coverage(wce1, width=230208) # make a track export(ip1.cov, "ip1_coverage.wig") > sessionInfo() R version 2.10.0 Under development (unstable) (2009-09-03 r49555) x86_64-unknown-linux-gnu locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] rtracklayer_1.5.13 RCurl_1.2-0 bitops_1.0-4.1 chipseq_0.1.25 [5] ShortRead_1.3.34 lattice_0.17-25 BSgenome_1.13.11 Biostrings_2.13.39 [9] IRanges_1.3.75 loaded via a namespace (and not attached): [1] Biobase_2.5.6 XML_2.6-0 grid_2.10.0 hwriter_1.1 -Chris Chris Seidel, Ph.D. http://research.stowers-institute.org/cws _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
