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ChIP-Seq: An integrated ChIP-seq analysis platform with customizable workflows. Newsbot! Literature Watch 0 07-09-2011 03:10 AM
ChIP-Seq: CASSys: an integrated software-system for the interactive analysis of ChIP- Newsbot! Literature Watch 0 06-29-2011 02:10 PM
PubMed: Using CisGenome to Analyze ChIP-chip and ChIP-seq Data. Newsbot! Literature Watch 0 03-15-2011 03:00 AM
Using CisGenome for ChIP-seq analysis Beginner Bioinformatics 2 04-19-2010 08:23 AM
PubMed: An integrated software system for analyzing ChIP-chip and ChIP-seq data. Newsbot! Literature Watch 0 11-04-2008 06:03 AM

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Old 02-10-2010, 08:53 AM   #21
tec
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Quote:
Originally Posted by tec View Post
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
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Old 03-04-2010, 12:49 PM   #22
dukevn
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Default 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.
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Old 03-16-2010, 11:19 AM   #23
honey
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Smile to find binidng motif in chip on chip data

I have nimblegen Chip on chip data with two antibodies and want to find out common binding motif from the data could anyone point me how to proceded I know there are several softwares -chipmotif, cisgenom etc.
The file I have has chr position marked 1000 bp (I combined probles of different regions) and then log ratio of intensities. How to create intial file meaning Bed or else. Do I have to put these chr positions in data in USCS genome browser to get seq out put but then what will happend to score. Apology fro asking such a trivial question.
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Old 06-23-2010, 08:20 AM   #24
lqscici
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Hello,

I am a rookie in applying cisgenome and now I have a problem in installing it in Linux. I have unzipped cisgenome v1.2 and entered the "cisgenome_project", after typing "makefile" it appears "-bash: makefile: command not found". If I change to run "make", I get the error "makefile:3: *** missing separator. Stop."

I don't know what to do, I have been searching through manuals and forums for weeks now. Any help would be greatly appreciated!

Thanks!
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Old 07-05-2010, 08:27 AM   #25
hklein
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Default compile cisgenome

Hi lqscici,

the problem is that the file "makefile" in cisgenome_project is not a file in proper Makefile format as a standard "make" command would expect it, but it's a shell script.
You can try a
Code:
./makefile
in the cisgenome_project folder (should work because of the "#! /bin/sh" in the first line), or you call it explicitely as a shell script:
Code:
sh makefile
I had some compilation problems related to 32/64 bit later on for ./cpp/tablesorter.cpp and ./cpp/tablesorter_str.cpp - I had to remove the "-m64" flag for the two targets before being able to compile. Just in case you get the same problem later on. Please be aware that I did not test if this has an effect on the results.

Cheers,
Holger
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Old 12-21-2010, 04:34 AM   #26
hathiram
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Smile

hello, i am using cisgenome for chip-chip data analysis.
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Old 12-21-2010, 04:47 AM   #27
hathiram
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hello everybody, I am using cisgenome for chip-chip data analysis. I am getting constant FDR .619523 for all ~900 potential binding regions in .cod file, using two sample analysis in TileMap, where I put sample > control.
can anybody tell me that why i m getting constsnt FDR for all 900 regions.

i willbe really highly thankful to all.
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Old 01-13-2011, 10:14 AM   #28
Husen
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Quote:
Originally Posted by hklein View Post
Hi lqscici,

the problem is that the file "makefile" in cisgenome_project is not a file in proper Makefile format as a standard "make" command would expect it, but it's a shell script.
You can try a
Code:
./makefile
in the cisgenome_project folder (should work because of the "#! /bin/sh" in the first line), or you call it explicitely as a shell script:
Code:
sh makefile
I had some compilation problems related to 32/64 bit later on for ./cpp/tablesorter.cpp and ./cpp/tablesorter_str.cpp - I had to remove the "-m64" flag for the two targets before being able to compile. Just in case you get the same problem later on. Please be aware that I did not test if this has an effect on the results.

Cheers,
Holger

Thanks for mentioning the CPU solution, it helped me a lot.
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Old 01-13-2011, 10:15 AM   #29
Husen
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Quote:
Originally Posted by hklein View Post
I had some compilation problems related to 32/64 bit later on for ./cpp/tablesorter.cpp and ./cpp/tablesorter_str.cpp - I had to remove the "-m64" flag for the two targets before being able to compile. Just in case you get the same problem later on. Please be aware that I did not test if this has an effect on the results.

Cheers,
Holger

Thanks for mentioning the CPU solution, it helped me a lot.
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Old 01-17-2011, 02:49 AM   #30
Husen
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Default cisGenome output (.bar or .cod) to .wig?

Quote:
Originally Posted by seidel View Post
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).

I need a similar program to convert sicGenome output (bar/cod) to wig, please let me know if you have got/developed such a tool.
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Old 01-20-2011, 03:00 PM   #31
hji
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Default cisgenome v2.0

We have just updated cisgenome to v2.0. BAR->Wig conversion is added. Two-sample ChIP-seq analysis algorithm updated which solves most of the memory problems we had previously.
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Old 01-21-2011, 11:25 AM   #32
tir_al
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Default Cisgenome V2 Genome selection

Dear Hji,

Could you please tell me in which way to choose the appropriate genome for my samples in cisgeome v2 on linux os?

I couldn't find the flag in the seqpeak application.

Reagards.
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Old 01-21-2011, 11:37 AM   #33
hji
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Default To tir_al

You don't need to choose a species/genome in v2 (seqpeak). The program will automatically determine the number of chromosomes and chromosome length. This way, it can be applied to all species. After you run the program, you get bar files, you then visualize those bar files with the genome annotation you want to use.
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Old 01-24-2011, 08:47 AM   #34
Husen
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Default can't build cisgenome from source code or can't execute it on Linux system

Hi,

I had a problem to execute cisgenome-2.0 under Linux (Ubuntu 10.10), but including the following package in tablesorter.cpp and tablesorter_str.cpp solved the problem.
Code:
#include <cstdio>
regards
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Old 01-24-2011, 09:11 AM   #35
hji
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Husen,

Thanks for providing a solution.

Quote:
Originally Posted by Husen View Post
Hi,

I had a problem to execute cisgenome-2.0 under Linux (Ubuntu 10.10), but including the following package in tablesorter.cpp and tablesorter_str.cpp solved the problem.
Code:
#include <cstdio>
regards
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Old 01-24-2011, 01:56 PM   #36
Husen
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Default Cutoff value for analyzing on-sample chip-seq data

Hi hji,

Could you please explain briefly how to set cutoff value (-c option) of the peak-detector for analyzing one-sample chip-seq data.

Based on section 3.4 of the user manual, FDR for each read count is given in output of windowsumarryv2 and the peak-detector is supposed to set a single value for the cutoff (-c) option. I wonder how this could be done or the default value (10) would be fine?

your answer is highly appreciated..
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Old 01-24-2011, 06:27 PM   #37
hji
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Default How to choose one-sample chip-seq cutoff

In the output of windowsummaryv2, go to the last column (negbinomial_exp/obs), find the first line with value < 0.1 (i.e. FDR < 10%), then go to the first column of this line, find the number c, use c as your cutoff. In the user manual webpage, you can find an example summarys1.txt in section 3.4. In this example, you will go to this line:

8 750 0.000024 0.000000 0.000000 0.000001 0.048812

The cutoff is 8.
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Old 01-25-2011, 03:01 AM   #38
Husen
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Thank you very much for your help hji.

Last edited by Husen; 02-03-2011 at 01:58 AM.
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Old 05-22-2011, 11:26 PM   #39
pd
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Hello Hji
I had a small query regarding retrieval of peak's sequences from cisgenome and UCSC. When i use the Get Sequence option in CisGenome, the fetched sequence from cisgenome never matches to the sequence which i get from UCSC. Any idea why is it so?

Last edited by pd; 05-22-2011 at 11:27 PM. Reason: Sequence differs when compared to UCSC
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Old 05-22-2011, 11:46 PM   #40
hji
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Default Re parveendabas:

You need to check and make sure you used correct genome assembly. For example, when the coordinates of your genomic regions are on human hg18, but you used hg19 genome in cisgenome, you cannot expect to get correct sequences, since hg18 and hg19 do not have the same coordinate system. Also, there might be 1 bp offset since we use 0-based index and UCSC may use 1-based index for coordinates. Other than that, I never encountered the problem you mentioned, and in our own analysis we always do a check by aligning a few retrieved sequences back to UCSC, and we always get the correct alignment.
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