How to transfer the BSP sequencing results into the standard legend? - (Aug/09/2006 )
I am a new and have a simple question about bisulfite sequencing PCR.
After amplification, cloning, and sequencing,how can I label the CpG islands of the sequence like this(the filled and open circles) below?.With which software I can do it?
Plz see the attachment
i suspect the figure was hand drawn with a program such as coreldraw or illustrator.
There is a program available on the web called BiQAnalyser that does something similar to this, see the online tools thread.
Nick
There is a program available on the web called BiQAnalyser that does something similar to this, see the online tools thread.
Nick
Thank you for your suggestions.But after carefully reading the guidelines of bio-analyzer,I found there is no introduction about how to creat the lollipop diagram.Can somebody else give me more information on this?
BlueBlack
You need to download the BiQ Analyser software and put your sequence data into it. It will eventually generate your lollipop diagram after you go through all the steps of the program. I must admit it takes a little bit of getting used to but once you master this program it's very good.
For those using this program I have found that if you copy and paste your generated "machine readable format" data into the BiQ diagrams webtool you get a better looking lollipop (the circles are bigger and stalks shorter) than that generated by the intitial program.
Blue black, if you can get your data into machine readable format I think you should be able to generate a diagram straight from the webpage.
Hi Blueblack
I've checked this for my own interest and you can generate lollipops without putting your data through the entire process.
Go to the BiQ analyzer diagrams link. See here
Cut and paste your data (from a txt file, word doc etc) into the blank box, select compressed, and then select generate diagrams and it should work.
Your data needs to be in the following format (1=meth CpG, 0=unmeth CpG). You need tabs between all numbers and the sequence name. The numbers between the CpGs is the base pair distance (if you don't want proportional distances between CpGs just enter the same number each time eg. 2) The first 2 and last 2 in each line is just to move the lollipops in from the edge of the diagram.
eg.
seq1 2 1 15 0 12 0 10 0 8 1 2
seq2 2 1 15 1 12 0 10 0 8 1 2
Try a simple sequence as above and see how you go.
Good luck!
many thanks to karyotyper
Actually,I have to bother you again because another problem comes out. I 've download the Bio-analyzer from the website but it totally didn't respond.The FAQ says there is a prerequisite for advanced java version.I followed and download another version(Java Runtime Environment (JRE) 5.0 Update 8) ,then double clicked the "start BiQ_Analyzer.bat" for windows system,but it's not sound yet
Please help me finish it .
BlueBlack
Hi again Blueblack
I had this exact same problem! I'm not much of an IT geek and I had to get our IT people to fix it for me but I think I recall how they did it. The BiQ_Analyzer folder that you download has to be sitting in your "Programs Files" folder.
Locate the folder you downloaded (called BiQ_Analyzer) and move it into the Programs Files folder. I think when the program launches it looks for the .exe file in C:\programs files\BiQ_Analyzer folder. If the folder is not located here it won't launch (at least that's what I think our IT guy said to me!)
Hope this helps.
As I said, you don't need the program to generate the lollipops, but i have found it's very useful for analyzing sequencing data. Try with a small number of sequences first.
All the best.
Dear karyotyper
I think I get it.
When the Bio-Analyzer file was released , I found there's two folders.Just keep one and copy it to your favorite directory.That OK.
Many thanks again.
BlueBlack
Blueblack if you copy the folder into your favourite directory then you will have to edit the .bat file accordingly, you can do this with notepad. All that is in this file is a line of command that will be executed. at the moment it's pointing to //Program Files/BiQAnalyser/ see below:
java -Xms64m -Xmx256m -cp BiQ_Analyzer.jar biq_analyzer.Frontend "c:\Program Files\BiQ_Analyzer\default.cfg"
because this .bat file is within the same folder as the BiQ_Analyzer.jar file there is no need to point java into a specific directory. The error comes where java can't find the default.cfg file (in red) because it's not in the directory specifed.
If you have copied the folder to a specific directory then you would have to change the part in red to your favourite directory. For example I have a specific Bioinformatics folder on my drive and it would become:
java -Xms64m -Xmx256m -cp BiQ_Analyzer.jar biq_analyzer.Frontend "c:\Bioinformatics\BiQ_Analyzer\default.cfg"
hope this helps.
Nick