[dukevn]

CisGenome does not run?

Hi all,

I can not make CisGenome to work on my system. I downloaded windows version, unzip, put it in C:\ and changed the ini file to the right location, but then when trying with some test files, nothing happened. It seems to me that the GUI does not connect with the executable files.

Any body has it run on your computer, can you help please?

Thanks,

D.

[tec]

Hello,

i have a problem concerning the cisgenome browser and the visualization of already analyzed ChIP-Seq data through the Linux version of Cisgenome.
When i want to visualize *.bar, *.genefile, *.cod, .... files, i always get a message - file doesn't exist!

When i call peaks with the Windows version of cisgenome and then doubleclick on a peak - the browser opens and the data is showing in the browser. But adding additional datafiles is not possible.. - file doesn't exist..!?

Are there any helpful suggestions???

Thanks! tec

ok, the problem is solved
we had to change the config file - src_filename=.. - to the right path of the file

[tec]

Cisgenome Browser - file doesn't exist

Hello,

i have a problem concerning the cisgenome browser and the visualization of already analyzed ChIP-Seq data through the Linux version of Cisgenome.
When i want to visualize *.bar, *.genefile, *.cod, .... files, i always get a message - file doesn't exist!

When i call peaks with the Windows version of cisgenome and then doubleclick on a peak - the browser opens and the data is showing in the browser. But adding additional datafiles is not possible.. - file doesn't exist..!?

Are there any helpful suggestions???

Thanks! tec

[ljul]

Hi all, I'm new here and am hoping someone may be able to help me out with a little Cisgenome issue I'm having. I've used Cisgenome successfully on a PC running Windows XP, but I'm now trying to run the program on my MacBook Pro using the Parallels program, which allows me to run Windows XP. I'm able to open the program through XP on my MAC and can load files as well, but when I try to run an application (right now I'm attempting Gibbs sampling) I get the quickly flashing black window that then disappears, and the program won't continue running. I have checked the file paths and file names, and there are no blank characters included anywhere. Also, the cisgenome.ini file does specify the correct Cisgenome installation path, so I'm at a loss as to what the problem is. Does anyone have experience running Cisgenome on Windows XP through MAC Parallels? Or perhaps it isn't possible to run the program this way. Thanks in advance, any assistance will be greatly appreciated.

[zhlyang]

Genome database file not listed on the website

Hi Hji, I am new in the NGS analysis and is going to try the Cisgenome. I need to use a small viral genome which is not listed on the Cisgenome genome database on the website. Would you mind to let me know the way to convert a Genbank genome to a Cisgenome database file?Thank you.

[hon]

How to convert eland_extended.txt format to Aln format in order to use the Cisgenome program?

[tebuffer]

motif files created but not showing up in project menu

In Windows, I load the genome database, genome region and coordinates and run "Annotate with ->Closest Gene". I get the output listed under the Project Explorer. Perfect so far.

When I run, "Get sequence" , the fasta file is generated, but it does not show up in the Project Explorer. Likewise, when I run the "New Motif Discovery" with the previously generated FASTA sequence file, motifs are discovered and stored in the location that I specified, but they do not appear under the "Project Explorer".

Would appreciate if anyone could point me to getting this correct.

Thanks,
TEB

[seidel]

convert bar to wig

Anyone know of a utility to convert .bar files to .wig files?

I'd be happy to write a program to do it - but any pointers for the .bar format would be helpful. I'm sure I'm not the only one who would be interested in seeing cisGenome output in the UCSC genome browser (which doesn't read .bar last I checked).

[schandri]

Thanks for your post, hji. Your suggestions fixed the problem! I had installed cisGenome in a path that did not have any spaces, but had made two other mistakes. First, the path in the .ini file was slightly off and second, my .COD data file was in a location that had a file path containing spaces. Now it seems to be working great!

Thanks again.
Sanjay

[hji]

schandri

First, check whether you have set the CisGenome.ini file. In that file, you should give the CisGenome installation path.

Second, check whether any of your folder or file path/names contains blank characters such as "C:\My Document\". If so, move (or rename) your data to folders that do not contain blank characters. CisGenome should also be installed in a folder that does not contain blank characters.

Try and see if this solves your problem.

[schandri]

cisGenome trouble shooting?

Hello,

I am trying to use cisGenome to "find closest gene" to TF binding sites identified using ChIP-Seq. I have downloaded the human genome database (hg18) and have converted the enriched sites into the COD file format. I was able to load the genome datase and COD file into the cisGenome browser. Then I choose “Genome > Annotate with … > Closest Gene”. From here I indicate a save to location and hit "OK". There is a new window that flashes (too fast for me to read) and then there is no file saved or further COD added to the project. I don't know what I am doing wrong. I would be EXTREMELY grateful for any advice.

Best regards,
Sanjay

[hji]

I just added a function to convert BED file to ALN file. You can then use the ALN file to detect peaks and perform subsequent analysis. You are certainly welcome to try CisGenome.

BTW, we have also added support for C elegans, Yeast and Chicken recently.

[tfcheng]

Hi HJI,
I am trying to analyze my chip-seq results, I am hoping that CisGenome can help me. I have two sets of data, experimental and control, both in WIG and BED formats. I need to know the difference between the two. Being a rookie in chip-seq field, do you mind telling me if CisGenome is the right tool for me? and if so, how should I use it? thank you!!

[hji]

In that case, I suggest you look at the raw data first. You can import the fc.bar and ma.bar into CisGenome browser and look at the top peaks. Ask yourself the question: do they look like something real? This will help you understand whether the FDR make sense or not.

Regarding why FDR are always grouped: because the FDR is forced to be monotone. Your peaks are ranked, the raw FDR is computed as (# peaks in the left tail)/(# peaks in the right tail). Suppose the raw FDR is: 0.01; 0.02; 0.00; 0.06; 0.05; 0.07 ... then the reported FDR will be 0.00; 0.00; 0.00; 0.05; 0.05; 0.07 ... This is somewhat like the Benjamini-Hochberg procedure.

[What_Da_Seq]

Sorry I did not make this clearer. Now that I have done a couple analyses I can tell you that I am not getting any peaks using HMM and 2 samples when comparing (treatment > control) and only like 20 peaks for (control > treatment). I have not used the UMS settings yet.
I was just wondering since I am looking for single base events (CpG or MeCpG) and not TF binding what would be my most relaxed (least stringent) HMM setting for peak detection. I can identify 3000+ regions via MA(300) for (treatment > control) but only 5 of these regions are FDR 0.0000000 and the next group of peaks is 0.10000000.
I also have no good grasp on why the FDR numbers in the COD files are grouped instead of continuous (eg. 5 peaks FDR=0.0000000, next peak group at 0.1000000).

I greatly appreciate your input. I am just trying to work my way through the 2005 TILEMAP paper. If only my statistical comprehension would be better. But the program so far is very nice especially since my boss always wanted some sort of FDR calculations incorporated into tiling analysis.

Thanks again