Hi, Is there any way to create directly track hubs from DMRcate output or DMPs of minfi to visualize them on UCSC?
Many thanks, Rahel
Hi Rahel,
You can export a GRanges object from DMRcate output with "extractRanges" function. After you get your Granges object, you can use rtracklayer library's "export.bed" function. Then you can add that BED file as a custom track on UCSC (under My Data menu).
For minfi DMPs, you first need to get the genomic locations of the probes. You can do two things. Although it has a lot of type conversions, the first one is the easier one I think. After filtering out your DMPs, get a subset of your original MethylSet object (or if you have already RatioSet, its better). After subsetting, convert your MethylSet object to RatioSet with "ratioConvert" function. Then, you can attach the genomic coordinates to your RatioSet object by "mapToGenome" function. Output of this function is a GenomicRatioSet object. You can create a GRanges object from GenomicRatioSet by simply calling "granges" function with your object. Rest of it the same with the DMRcate (i.e. "export.bed" function).
The second way is to download the 450k manifest from Illumina in CSV format. Load that into R, and get the coordinates of your DMPs and write the chromosome, start-1, start, probe name, ., and strand information as a tab separated file. This will be in BED format, so you can load it again in the UCSC genome browser.
Hope this helps,
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Dear asyavuz, Many thanks for your explanation. I already have the DMRs.bed and DMRs.bw and I almost got them with the same way as you explained ... I also uploaded them on Dropbox to make a public url from data and make a custom track line ... but it gives me error and my main problem is to upload the bigwig file to a public server bcs dropbox is not working. As I need to share this trackDB.txt ... Do you have any idea for this part? Kind Regards, Rahel
This may sound too obvious, but did you try uploading directly to the UCSC genome browser? Is your file too big?
yes it is a big file in bigwig format and it is asking me to upload it on a public host ...
big* files (bigBeds, bigWigs, bams, bigPsl, bigMaf, etc) need to be hosted on an ftp, http, or https server that enables byte range requests so we can efficiently access the file. If your files are small enough, and you don't have any web space available through an institution or something, you should consider converting your bigWig file to a wig using the bigWigToWig program and then uploading the wiggle file as a custom track.
If your file is indeed too large, you can look into hosting your data at CyVerse, an NSF funded website for helping genomics researchers. Please see this mailing list response for more information on hosting UCSC accessible data at CyVerse: https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/_Ws2jxNfJV4/0c5aGb_PAQAJ
The problem with hosting files at dropbox is that dropbox does not allow byte-range access to their files, same with google drive and most other free hosting services.
If you have any more questions about the UCSC Genome Browser, feel free to send your question to our public mailing list at genome@soe.ucsc.edu so our whole team can see your question. If your question involves private data, you can send it to genome-www@soe.ucsc.edu instead.
Thanks, ChrisL from the UCSC Genome Browser
Many many thanks for your explanation and reply. I will try to upload the .bigwig files on CyVerse and If it did not work, I will send you an e-Mail. Kind Regards, Rahel