[honey]

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

[gntc]

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.

[harishrk]

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 :-)

[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

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.

[harishrk]

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

[pd]

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

[gntc]

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

[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

[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.

[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

[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.

[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]

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 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?

[Husen]

Thank you very much for your help hji.