On Tue, Mar 23, 2010 at 4:46 PM, Chen-Yi Chen <[email protected]> wrote:
> Hi all, > Recently we found the greatness of this bioconductor ht-seq pacakage and > we would like to do some analysis in this package. We have aligned our > ChIP and input data by Bowtie aligner and try to output wig file for the > coverage, so we are able to use UCSC genome browser to visualize them. By > searching the documentation and work flow online, I found this great > thread in bioc-sig-sequencing archive: > > > https://stat.ethz.ch/pipermail/bioc-sig-sequencing/2009-September/000632.html > > We basically followed the work flow in the above thread, with some > slightly modifications: > ChIPread = readAligned("./", pattern="0_Rad_H3K4_ChIP.out", type="Bowtie") > ChIP = as(ChIPread, "GenomeData") > inputread = readAligned('./', pattern='0_Rad_input.out', type='Bowtie') > input = as(inputread, "GenomeData") > gdlist = GenomeDataList(list(input=input, ChIP=ChIP)) > input1 = extendReads(gdlist$input$chr1, seqLen=200) > ChIP1 = extendReads(gdlist$ChIP$chr1, seqLen=200) > library(BSgenome.Hsapiens.UCSC.hg18) > human.chromlens = seqlengths(Hsapiens) > input1.cov = coverage(input1, width=human.chromlens['chr1']) > ChIP1.cov = coverage(ChIP1, width=human.chromlens['chr1']) > inputrange1 = IRanges(start=start(input1.cov), end=end(input1.cov)) > score = runValue(input1.cov) > chr1 = rep("chr1", length(inputrange1))# > export(GenomicData(inputrange1, score, chrom=chr1), "input_test.wig") > > We successfully got a wig file output, however, when we try to visualize > it on UCSC genome browser, the peaks won't display correctly. > Could you please give a little more detail? A screenshot perhaps? > I took a glance on the output wig file, it has the format like the > following: > track name="R Track" type=wiggle_0 > variableStep chrom=chr1 span=1 > 251 7 > 395 7 > 14041 3 > 78204 1 > ... > variableStep chrom=chr1 span=2 > 12 2 > 212 9 > 346 7 > ... > variableStep chrom=chr1 span=3 > 343 8 > 404 7 > ... > ... > fixedStep chrom=chr1 start=117727703 step=129030611 span=1990 > 0 > 0 > variableStep chrom=chr1 span=1991 > ... > > Apparently the output wig file format we got is different than what's > mentioned in the thread, and I believed those different variable steps and > fixed steps are confusing the UCSC genome browser. > I would hope not. It looks like valid WIG. It's compressing the data using multiple variableStep and fixedStep blocks. > Is there a way to output the wig file in the format without all those > steps, for example, > track name="R Track" type=wiggle_0 > chrI 0 2 169 > chrI 2 4 176 > chrI 4 5 178 > chrI 5 7 179 > ... > which mentioned in the thread? > > This is no longer valid WIG. It's now called bedGraph. So you can export(track, "input_test.bedGraph"). But I'd like to figure out the problem with the WIG, if possible. Thanks, Michael > Thanks for your help! > > -Charlie- > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
