On Tue, Mar 23, 2010 at 5:24 PM, Chen-Yi Chen <[email protected]> wrote:
> > > ----- Original Message ----- > From: Michael Lawrence <[email protected]> > Date: Tuesday, March 23, 2010 4:57 pm > Subject: Re: [Bioc-sig-seq] Questions about coverage visualization in wig > file output > To: Chen-Yi Chen <[email protected]> > Cc: [email protected] > > > 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 attached a UCSC genome browser screen shot. > Thanks, but it's not clear what's wrong there. You're looking at an entire chromosome in heatmap mode. Could you maybe describe in words what's wrong? > > > > > > > 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. > > > I believed so too, but I've also emailed the supports in UCSC genome > browser. They said that usually WIG file only has very few number of > "variable steps", and the fixedSteps in our output WIG file didn't make > sense. > > This is probably because people rarely try to encode coverage in WIG, given bedGraph. Could you be a bit more specific about how the fixedSteps don't make sense? Thanks, Michael > > > > > 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"). > Thanks Michael! > The coverage graph displays pretty well in bedGraph format! > > Thanks, > -Charlie- > > > > > 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
