[Useq-users] USeq output formats and IGB loading tips

[David N. <Dav...@hc...>]

Sounds like you're trying to load up whole chromosomes of track data.  Best to use a DAS2 server like GenoPub and serve slices.  All browsers will choke when you load millions of data points.  By default IGB starts with the whole of chr1 open, you should zoom into a small region, say by clicking one of the html links in the excel output from the EnrichedRegionMaker.  Then load your data. Don't use the xxx.useq format for local file loading, use the xxx.bar files and only load the chromosome of interest after zooming in on a particular region.  I haven't implemented sliced local file loading for xxx.useq in the latest IGB release, this is coming.

If you like I can make you a trial account on our GenoPub DAS/2 server where you can upload data (after converting to xxx.useq format, see Bar2USeq) and then visualize slices in IGB. Let me know what university/ lab/ company your with , a phone contact number, etc. You can also install your own GenoPub server (recommended).  See http://bioserver.hci.utah.edu/BioInfo/index.php/Software:DAS2 for details.

I'd recommend using a 64bit computer with > 4G ram.

IGB is, in my opinion, the best genome browser available, no other comes even close to matching it's sophistication and data manipulation tool set.

I like UCSC for it's data not it's display or graph manipulation capabilities.  That said, check out their wig, bigwig, and bigbed file formats.  It's pretty easy to convert bar files to gr format (Bar2Gr) and then with a bit of parsing to make wig files that can then be converted to bigwig using UCSC's tools and visualized as custom tracks.

-cheers, David


--
David Austin Nix, PhD | Bioinformatics Shared Resource | Huntsman Cancer Institute | 2000 Circle of Hope | SLC, UT 84112 | Rm: 3165 | Vc: 801.587.4611 | Fx: 801.585.6458 | dav...@hc... | Skype/iChat: LiveNix | WebSite: http://bioserver.hci.utah.edu | DAS/2: http://bioserver.hci.utah.edu:8080/DAS2DB/genome



On 8/11/10 2:39 AM, "Anuj Pahwa" <anu...@an...> wrote:

Gday David,

I have just been playing around with the useq suite of applications (particularly ChIPSeq) and am interested in the outputs that are generated from that application. I know that you can generate BAR files and USEQ format files which IGB can handle and you can also generate bed files which UCSC can handle. I tried using IGB, but on the machines that I am trying it on, it is painfully slow, extremely memory and cpu intensive and not really usable (I have tried it on a machine with 4GB of RAM). Have you experienced such difficulties in performance with IGB? And do you have any recommendations on how to proceed with using UCSC? (Bed files that are generated are too big - approximately 1.2GBs and uploading them is not really an option)

Thanks for your help in advance,

Best wishes,

Anuj