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Search: Posts Made By: stefanoberri
Forum: Bioinformatics 02-18-2016, 03:43 AM
Replies: 1
Views: 620
Posted By stefanoberri
Hi. It is partially a loop. We provided a...

Hi.

It is partially a loop. We provided a solution with CNAnorm a tool described in this paper
http://www.ncbi.nlm.nih.gov/pubmed?term=22039209
but we awknoledge that there is not a single...
Forum: General 05-15-2013, 08:34 AM
Replies: 26
Views: 3,357
Posted By stefanoberri
"In theory" it could be possible, but there are...

"In theory" it could be possible, but there are many serious obstacles to overcome.

At the moment "reading" the genetic code of a cell is disruptive. You need to process the DNA in such a way that...
Forum: Literature Watch 01-07-2013, 01:01 AM
Replies: 25
Views: 6,779
Posted By stefanoberri
I am not sure what you mean. "merging adjacent...

I am not sure what you mean. "merging adjacent windows and reporting mean ratio" is usually called segmentation and CNAnorm performs segmentation too (using DNAcopy).
In the file resulted from...
Forum: Literature Watch 01-07-2013, 12:14 AM
Replies: 25
Views: 6,779
Posted By stefanoberri
Hi. I am afraid not. and the problem is in...

Hi. I am afraid not. and the problem is in "similar adjacent windows". It is difficult to decide what is "similar" and what is "different enough".

what is, more precicely, the problem you have?...
Forum: Bioinformatics 08-15-2012, 07:22 AM
Replies: 4
Views: 2,334
Posted By stefanoberri
Hi, sorry for the late reply. Here you can...

Hi, sorry for the late reply.

Here you can find the preprint of the article (http://dl.dropbox.com/u/23393292/preprint/Bioinformatics-2011-Gusnanto-bioinformatics_btr593.pdf) and the supplemental...
Forum: Bioinformatics 08-10-2012, 12:49 AM
Replies: 4
Views: 2,334
Posted By stefanoberri
Hi I am the developer of CNAnorm...

Hi

I am the developer of CNAnorm (http://www.precancer.leeds.ac.uk/software-and-datasets/cnanorm/) which is designed for normalisation, segmentation, GC correction and plotting of copy number data...
Forum: Illumina/Solexa 04-28-2012, 01:40 AM
Replies: 6
Views: 3,532
Posted By stefanoberri
The PCR increases the total number of DNA...

The PCR increases the total number of DNA fragments, but you do not sequence the same molecule twice (because you sequence a very small subset of the available ones). If you still are worried, you...
Forum: Bioinformatics 04-27-2012, 02:14 AM
Replies: 2
Views: 1,315
Posted By stefanoberri
Hi. I think the answer to your question...

Hi.

I think the answer to your question depends on the coverage you have.

We have some experience with low coverage CNV detection in tumour...
Forum: Illumina/Solexa 04-27-2012, 02:04 AM
Replies: 6
Views: 3,532
Posted By stefanoberri
hi antu82, I would suggest you to give a...

hi antu82,

I would suggest you to give a look at CNAnorm (http://www.precancer.leeds.ac.uk/software-and-datasets/cnanorm/) (here the paper that describe it...
Forum: Literature Watch 02-02-2012, 01:53 PM
Replies: 25
Views: 6,779
Posted By stefanoberri
No, unfortunately I haven't thought about...

No, unfortunately I haven't thought about parallel approach at the design stage. However, here a suggestion on how to make it fast and yet have high resolution.

From the same bam files, you...
Forum: Literature Watch 02-02-2012, 08:00 AM
Replies: 25
Views: 6,779
Posted By stefanoberri
I am not sure I understand what you mean. How...

I am not sure I understand what you mean. How about

exportTable(CN, file = "CNAnorm_table.tab", show = 'ploidy')

It will produce a tab file with chromosome, position, ratio... and segmented...
Forum: Literature Watch 01-25-2012, 08:40 AM
Replies: 25
Views: 6,779
Posted By stefanoberri
Hi. To start, I would suggest to skip the...

Hi.
To start, I would suggest to skip the smoothing step.

CN <- addSmooth(CN, lambda = 7)

If you have very high coverage, the signal should be already well smoothed, and further decresing...
Forum: General 01-23-2012, 12:07 PM
Replies: 2
Views: 1,216
Posted By stefanoberri
Hi. I am pleased to see that CNAnorm is...

Hi.

I am pleased to see that CNAnorm is considered also outside the task it was designed for.
We are using CNAnorm for high coverage data and we do have a couple of capture experiments we'll be...
Forum: Literature Watch 01-18-2012, 06:35 AM
Replies: 25
Views: 6,779
Posted By stefanoberri
It looks like you have something strange on line...

It looks like you have something strange on line 576287280 of your GC file (maybe last line?) probably "\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0..."



The size of the final tab...
Forum: Literature Watch 01-13-2012, 06:19 AM
Replies: 25
Views: 6,779
Posted By stefanoberri
Hi dmacmillan, I looked at the files you...

Hi dmacmillan,

I looked at the files you sent me to figure out why they didn't work. The problem had to do with the reference genome you use that is different to what I was using. I had...
Forum: Literature Watch 01-09-2012, 07:22 AM
Replies: 25
Views: 6,779
Posted By stefanoberri
You now need to use Bioconductor, see the webpage...

You now need to use Bioconductor, see the webpage (http://www.bioconductor.org/packages/devel/bioc/html/CNAnorm.html) and vignette...
Forum: Literature Watch 01-09-2012, 01:20 AM
Replies: 25
Views: 6,779
Posted By stefanoberri
Good, we are making progress. If you provide 2...

Good, we are making progress. If you provide 2 very small bam files that still produce the errors (I guess it is a warning) I'll try and fix it.

I suspect, however, this is unrelated to the first...
Forum: Literature Watch 01-06-2012, 08:20 AM
Replies: 25
Views: 6,779
Posted By stefanoberri
Hi. How big are they? CNAnorm was designed...

Hi.

How big are they? CNAnorm was designed for low coverage, however I am now using it for high coverage (30X) without problems. I would suggest you do not use the default 30 reads per window with...
Forum: Literature Watch 01-06-2012, 07:58 AM
Replies: 25
Views: 6,779
Posted By stefanoberri
Hi. This is the first time this error is...

Hi.
This is the first time this error is reported.
you'd need to help me a bit more
- what platform are you using (operative system, version of Perl...)
- Report the exact error as provided by...
Forum: Illumina/Solexa 12-07-2011, 12:41 AM
Replies: 4
Views: 4,211
Posted By stefanoberri
Hi. We observed that read coverage is...

Hi.

We observed that read coverage is affected by GC content. Each sample, however, have a different bias and has to be corrected independently. We don't know exaclty why, and we suspect it is...
Forum: Literature Watch 11-18-2011, 01:10 AM
Replies: 25
Views: 6,779
Posted By stefanoberri
CNANorm: A normalization method for Copy Number Aberration in cancer samples.

CNAnorm performs ratio, GC content correction and normalization of data obtained using low coverage (one read every 100-10,000 bp) high throughput sequencing. It performs a "discrete" normalization...
Forum: Bioinformatics 08-24-2011, 12:07 PM
Replies: 2
Views: 2,238
Posted By stefanoberri
I'd like to know this answer as well. As far...

I'd like to know this answer as well.

As far as I understand, if one of the two has uniq mapping, than the pair has unique mapping (maybe not, it could be that the second one can map in two very...
Forum: General 08-24-2011, 07:48 AM
Replies: 12
Views: 2,278
Posted By stefanoberri
that's right

that's right
Forum: General 08-24-2011, 07:33 AM
Replies: 12
Views: 2,278
Posted By stefanoberri
... So, that link is right, but inclomplete...

...

So, that link is right, but inclomplete as it assumes you know DNA is double stranded but just does not write the other strand, because you can get it yourself.
Here how it would look like...
Forum: General 08-24-2011, 06:55 AM
Replies: 12
Views: 2,278
Posted By stefanoberri
either if you find a heterozygous SNP, it...

either

if you find a heterozygous SNP, it means one of the two chromosomes, for that position, had a nucleotide different from the reference genome. If it is a homozigous SNP it means that both...
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