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Software tools for detecting Copy Number Variations (CNV) smice Bioinformatics 24 11-10-2014 02:59 AM
CNV Simulator -- Random Number Generation gprakhar Bioinformatics 5 05-11-2012 10:34 PM
tools to detect copy number variants nans_bn Bioinformatics 2 01-12-2012 05:25 AM
PubMed: Detecting copy number variation with mated short reads. Newsbot! Literature Watch 0 02-18-2011 12:00 PM
CNV variation effects on exome sequencing? wrighth Bioinformatics 0 12-21-2010 12:43 PM

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Old 07-17-2014, 08:03 AM   #41
clarissaboschi
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Quote:
Originally Posted by arcolombo698 View Post
@ Clarissa

normally with CGH experiments you are comparing a tumor sample with a non-tumor sample. my data has a germline sample and also a tumor sample. the germline is used as a reference. So you should have two samples to compare.

?
@arcolombo698
Thanks for the response.
In my experiment I have 2 different chickens lines - broiler x layer. But I have individual samples from broilers and layers. Should I combine all my broilers and layers? But I want to check in each sample (chicken). I have 10 broilers and 10 layers. I dont have a control sample. So maybe I need a control from another chicken line? I am not sure because in my experiment I detect SNPs using a reference from NCBI (chicken reference genome).
Any suggestions?
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Old 07-21-2014, 05:06 PM   #42
arcolombo698
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I am not a CGH expert by any means whatsoever. From my experiments, the germline samples are the controls, which are tumor free. The tumor samples have tumors, and we are measuring the variation between the two.

My best advice, is to go onto PubMed and find experiments similar to you. It depends on your experiment design and hypothesis. I am under the impression that the reference is the control. I am also not an expert with chicken experiments, I have only worked on hg19, and mm10 for NBL, and Medullo.

if you use the layer as the reference, the CNV data that will be output is in relation to the broiler changes with respect to layer. This just depends on your experiment design.
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Old 07-21-2014, 05:59 PM   #43
arcolombo698
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thank you for the response. What does the CNV argument mean? and what does the glim argument mean? is the glim the limits on the p.value column in the data frame for data?

From the manual...

plot.cnv.chr <- function (data, chromosome = NA,
from = NA, to = NA, title = NA,
ylim = c(-4, 4), glim = c(NA, NA),
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Old 07-23-2014, 06:43 PM   #44
arcolombo698
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Default Understanding the Log2 Ratio plotted

Hi. thank you in advance.
so after re-reading the manual, I have a question about the values for the y-axis.

The y-axis has the log2 data from the output in the .cnv file.

In the paper, it gives the predicted copy number r = z*(N_Y)/(N_X) .... is the values for r, the same values as the log2 column entries that is plotted on the y axis?

For instance, I am trying to interpret the ratio correctly.. given this test example

Since I use a reference/control (N_Y), and a tumor sample (N_X), from the original paper Xiao published, the positive log2 values indicate that (N_Y > N_X) which means that it was not an increase in copy number. is this correct understanding of the log2 value for their ratio?
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File Type: pdf test.pdf (6.5 KB, 10 views)
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Old 10-20-2015, 01:56 AM   #45
Alicia B
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Originally Posted by clarissaboschi View Post
Dear members,

I am using data from Illumina next generation sequencing from different chickens. I have different bam files (for each chicken), and I obtained the test.hits using the command line:
samtools view –F 4 file1.bam | perl –lane ‘print “$F[2]\t$F[3]”’ > test1.hits

But I need to have also the ref.hits, but I only have the reference chicken genome reference (fasta file). How can I get this ref.hits?

Thanks
Clarissa
@clarissaboschi did you ever find a solution to your question regarding what to use as a a ref-hits file? I am in what seems to be a similar situation to yours: I don't have a control sample and I am only trying to detect CNVs in various individuals (rice) comparing it to the reference genome. What did you end up doing?

Thanks for your help!
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Old 10-20-2015, 03:13 AM   #46
jflores
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Hello Alicia,

The most straight forward design you can employ here is to simply choose one of your test#.hits files as the reference. You can use the sample with the highest coverage as reference, or a sample that has been used before as reference in other studies, etc. Then you go on comparing all the rest of the chicken samples against this sample and obtain CNV calls relative to this sample. Let's say you choose test1.hits as the reference:

test2.hits vs test1.hits

test3.hits vs test1.hits

test4.hits vs test1.hits

....

Hope it helps,
Rodrigo F.
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Old 10-20-2015, 10:30 AM   #47
clarissaboschi
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Alicia, I gave up to use CNV-seq tool and I am using CNVnator which I do not need any reference.
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