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. 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. 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? Thanks for your help! -Charlie- _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
