Question for converting format of file

[Ajay Singhal]

Hello,

I am trying to convert TCGA data file into bed graph format, How can I achieve that? Please help.

Regards

AS

[Jonathan Casper]

Hello Ajay,

Thank you for your question about converting data into the bedGraph format. If it helps, the bedGraph format is described at http://genome.ucsc.edu/goldenPath/help/bedgraph.html. We are happy to help you further with this; we provide several tools for working with bedGraph files. Can you tell us more about the format of your TCGA data?

Please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

--
Jonathan Casper
UCSC Genome Bioinformatics Group

--

[Ajay Singhal]

Thanks a lot for reply. Actually I am trying to plot Log2 ratio vs Chromosome no but having problem in reading file. Please see attached file. I read somewhere that if the file is converted to bedgraph it is easy to plot. Please can I get help.

Thanks,

AS

[Jonathan Casper]

Hello Ajay,

There are a lot of data in your .xls file, and it's not immediately clear which pieces you are trying to graph. Are you trying to plot the values in the "logRatio" row against the names and positions that appear in the SystematicName row? If so, the spreadsheet program that you are using to read the .xls file probably has a "graph" (or "chart") tool that will be much easier for you to use. The bedGraph format is generally used for graphing a value that changes along a single chromosome, not for comparing different chromosomes. We do have a Genome Graphs tool (http://genome.ucsc.edu/cgi-bin/hgGenome) that displays data on multiple chromosomes at once, but it is also designed to show values that change over the span of each chromosome. Genome Graphs would not be the right tool when associating a single unchanging value with each chromosome.

If your problem instead is that you are unable to read the .xls file, we suggest that you search online for software that will allow you to open it. Without making any particular recommendations, among the software that will do this are Microsoft Excel, LibreOffice, and Google Docs (an online service).

You may also be interested in posting your question on a more general bioinformatics discussion site like https://www.biostars.org/. This mailing list is devoted to questions regarding the use of the UCSC Genome Browser and its tools; questions on how to interpret TCGA data are a bit outside of our scope.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

--
Jonathan Casper
UCSC Genome Bioinformatics Group