[Bioc-sig-seq] Questions about coverage visualization in wig file output

[Chen-Yi Chen]

----- Original Message -----
From: Michael Lawrence <lawrence.michael at gene.com>
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 <ChenYiChen at lbl.gov>
Cc: bioc-sig-sequencing at r-project.org

> On Tue, Mar 23, 2010 at 4:46 PM, Chen-Yi Chen <ChenYiChen at lbl.gov> 
> 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.
> 
> 
> > 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.

> 
> > 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
> > Bioc-sig-sequencing at r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
> >
> 
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