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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 05-24-2011, 03:52 AM   #41
pd
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Default 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?
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Old 05-24-2011, 10:35 AM   #42
hji
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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.
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Old 05-26-2011, 06:15 AM   #43
katsuda
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Default 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
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Old 06-01-2011, 02:07 AM   #44
Tanushree
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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.
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Old 06-08-2011, 10:35 AM   #45
Daydream
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Default 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
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Old 06-29-2011, 02:59 PM   #46
gntc
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Default missing files

Hello,

I am having trouble with CisGenome. Whenever I try to do anything that involves generating a file the file never appears. I have changed the .ini file. CisGenome is in a path that has no spaces. There are programs in the bin folder. But whenever I do something like a file conversion, or gene annotaion, the cmd box flashes on the screen then disappears and no files appear. Any suggestions?

gntc
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Old 07-29-2011, 05:50 AM   #47
pd
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Default Too many peaks generated using Cisgenome V2 (seqpeak)

Hi friends
I have a strange query. I ran cisgenome for single Lane alone and in replicates as well with Input DNA as control. The problem which i'm is regarding the number of peaks. When i use the Cisgenome V2 (new and recommneded, thats what software says) with default parameters, i got around 2,10,000 peaks (for one lane) and 1,90,000 (for 2 replicates). If i increase the "Win Stat Cutoff C >=" from 3 to 4 then the peak count decreses to 70,000 and if i keep the same option to 5, then peak count comes to 67. Shall i use the new version or not. Its fast but the output which is coming is impractical. Please clear the doubts Mr Hji
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Old 11-02-2011, 06:26 PM   #48
harishrk
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Default

Quote:
Originally Posted by gntc View Post
Hello,

I am having trouble with CisGenome. Whenever I try to do anything that involves generating a file the file never appears. I have changed the .ini file. CisGenome is in a path that has no spaces. There are programs in the bin folder. But whenever I do something like a file conversion, or gene annotaion, the cmd box flashes on the screen then disappears and no files appear. Any suggestions?

gntc
Hi,
I am having the exact same issue. Everything is according to the tutorial (no spaces etc.). The program launches fine and I have downloaded the rat genome. My Chip-seq data is in the Fastq format and I have converted it to aln (or atleast I think the conversion has happened since I see a file with that extension and it is a big file, thoughsmaller than the Fastq file). When I run it spits out a blank window and the command box just flashes and disappears. Any help would be greatly appreciated.
Thanx.
hk
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Old 11-07-2011, 10:13 AM   #49
gntc
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Quote:
Originally Posted by harishrk View Post
Hi,
I am having the exact same issue. Everything is according to the tutorial (no spaces etc.). The program launches fine and I have downloaded the rat genome. My Chip-seq data is in the Fastq format and I have converted it to aln (or atleast I think the conversion has happened since I see a file with that extension and it is a big file, thoughsmaller than the Fastq file). When I run it spits out a blank window and the command box just flashes and disappears. Any help would be greatly appreciated.
Thanx.
hk
Harishrk,

What are you trying to do exactly?

First, when the command box flashes and disappears it means there was an error. Cisgenome doesn't say what the error was, it just terminates the program. It could be that you didn't set a proper output destination and title, the input was in an incorrect format, or that the commands (or input and output) are in a path that has spaces in it. For some reason Cisgenome doesn't work if the Desktop is in the path, so make sure to put it somewhere else.

Secondly, aln files show genomic regions that sequences have mapped to after alignment with a program like bowtie. You should not be able to convert a fastq file to aln. Fastq files only contain the sequences and the quality of the read, no information about alignment. If you converted fastq to aln I would guess that this is your problem. You must first map your sequences to the genome, then you can convert that output to aln.
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Old 11-07-2011, 11:29 AM   #50
harishrk
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Quote:
Originally Posted by gntc View Post
Harishrk,

What are you trying to do exactly?

First, when the command box flashes and disappears it means there was an error. Cisgenome doesn't say what the error was, it just terminates the program. It could be that you didn't set a proper output destination and title, the input was in an incorrect format, or that the commands (or input and output) are in a path that has spaces in it. For some reason Cisgenome doesn't work if the Desktop is in the path, so make sure to put it somewhere else.

Secondly, aln files show genomic regions that sequences have mapped to after alignment with a program like bowtie. You should not be able to convert a fastq file to aln. Fastq files only contain the sequences and the quality of the read, no information about alignment. If you converted fastq to aln I would guess that this is your problem. You must first map your sequences to the genome, then you can convert that output to aln.
Thanx for the detailed info. I think I may be able to fix it now bcos I took the original FastQ file and converted it into aln. I was under the assumption that since I provided the Rat genome (rn4) this program also does the alignment (similar to bowtie) and then calls the peaks. I will try now with the bowtie output. How do I convert the bowtie output to aln in that case? Sorry for all the newb questions :-)
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Old 11-07-2011, 01:12 PM   #51
gntc
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Quote:
Originally Posted by harishrk View Post
Thanx for the detailed info. I think I may be able to fix it now bcos I took the original FastQ file and converted it into aln. I was under the assumption that since I provided the Rat genome (rn4) this program also does the alignment (similar to bowtie) and then calls the peaks. I will try now with the bowtie output. How do I convert the bowtie output to aln in that case? Sorry for all the newb questions :-)
Try reading the manual.
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Old 11-07-2011, 01:55 PM   #52
honey
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Default BRA file format

I have BAM files after BWa alignments will it be compatible with Cis genome it says BRA format. How to get that format. I can convert BAM to SAM
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Old 11-18-2011, 04:07 PM   #53
townway
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Hi all,

I am using latest Cisgenome (windows version) to call Chi-seq peaks. But I got the errors when I used "Two sample peak calling (New and recommend)". After I added my IP and input file in aln format and used default setting, I got the error window "cannot write sample list to argument file!"

Would you tell me what the problem is ? I also tried the demo data, the same happened.

Thank you so much

Wei
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Old 11-21-2011, 11:02 AM   #54
gntc
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Honey,

You can convert like this:

BAM -> BED -> ALN

Then use the ALN file with the peak calling to get a BAR file. I use the bedtools package to convert bam to bed and cisgenome to convert bed to aln.
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Old 11-21-2011, 11:24 AM   #55
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yes dear, I am doing extactly the same

but cisgenome(windows version) seems not like my PC, so I switched to linux version on our cluster and it worked.

I wonder it might be a bug of windows version.

Quote:
Originally Posted by gntc View Post
Honey,

You can convert like this:

BAM -> BED -> ALN

Then use the ALN file with the peak calling to get a BAR file. I use the bedtools package to convert bam to bed and cisgenome to convert bed to aln.
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Old 11-23-2011, 09:17 AM   #56
gntc
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Quote:
Originally Posted by townway View Post
yes dear, I am doing extactly the same

but cisgenome(windows version) seems not like my PC, so I switched to linux version on our cluster and it worked.

I wonder it might be a bug of windows version.
Haha, yes dear.

The windows version is buggy and annoying. Good to know that I'm not the only one doing what I'm doing and having problems with the windows version.
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Old 11-23-2011, 09:21 AM   #57
gntc
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Does anyone know why when running One Sample Peak Calling Peak Detection with Boundary Refinement and Single Strand Filtering selected no .cod file is created? When I run this with my data I get 6 new files:

title.bar
title.cgw
title_F.bar
title_F.cgw
titlle_R.bar.tmp
title_R.regtmp

The .tmp files suggest to me that maybe the program is crashing. Has anyone else experienced this?
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Old 11-23-2011, 09:51 AM   #58
honey
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I agree cisgenome is probably created by a lInux reseacher and they never cared it has to be used by biologists. I wasted lot of time and end up using Cistrome they need to look into that. They even dont respond emails. That is bit annoying.... sorry but it is true.. If you can not support community then take off your software from public claims
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Old 02-10-2012, 12:30 PM   #59
Bas
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Quote:
Originally Posted by ljul View Post
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.
Hi everybody, I just started using Cisgenome and was hoping to run it on my Mac using Parallels. However, I'm experiencing similar problems and was hoping anybody has a clue how to overcome this issue?

Cheers,

Bas
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Old 02-13-2012, 08:06 AM   #60
mudshark
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why not running it under OSX natively, i.e. Darwin??
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