[hji]

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.

[tir_al]

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.

[hji]

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.

[Husen]

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.

#include <cstdio>

regards

[hji]

Husen,

Thanks for providing a solution.

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.

#include <cstdio>

regards

[Husen]

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..

[hji]

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.

[Husen]

Thank you very much for your help hji.

[pd]

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?

[hji]

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.

[pd]

Hello Hji

I had already cross checked both the things which you have mentioned that is a) Using the same build e.g. hg18 in both Cisgenome and UCSC and b) considering the offset of 1. But i still get the different sequences. Any idea?

[hji]

How many sequences have you tried, and how long are they? What % of them are correctly aligned? Are they repetitive sequences? If the results do not make sense after you have considered all these factors, you can send me a few genomic regions for me to try.

[katsuda]

CisGenome for plant species

Hello hji,

I am a beginner in this field.
I would like to try CisGenome for the analysis of my ChIP-seq data from rice.
I would be grateful if you could tell me whether it is possible to analyze rice data by CisGenome?

Regards,

katsuda

[Tanushree]

Hello!!!
I have used bioscope for mapping of chipseq data, then used cisgenome for making the .aln , .cod, .cgw and many more files. Can any one tel me the steps to visualize the peaks using cisgenome browser. From where does .ini files.
Any help will be appreciable.

[Daydream]

does it work with data file in text or bigBED format?

Hi forum

I just got my first CHIP-seq data back and needed to find a way to get a list of enriched genes. I stumbled upon Cisgenome and was so glad that this might be it. However, I encountered several problems and am in need of help to resolve them.
First, when I download the Cisgenome V2.0 for windows, I could not find the exe and ini files after de-compressed the tar file with 7-Zip. However, it seems that I can still have the working windows opened fine. I am not sure whether I installed the software correctly?
Second, all my data are in text or bigBED format (core facility only provided data in text/bigBED/bigWig format) and I could not find a way to convert them into aln format. Could anyone please help with how to convert from text file into aln file?
Third, the piled hg19 genome database is for unix OS. I don't seem to be able to de-compressed it under windows OS. However, I can upload the file to Cisgenome. Can anyone tel me if this will work or direct me to the place where I can download piled hg19 database for windows?

Thank you very mcuh