Forum: Bioinformatics
02-18-2016, 04:43 AM
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Replies: 1
Views: 1,051
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...
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Forum: General
05-15-2013, 09:34 AM
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Replies: 26
Views: 5,148
"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...
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Forum: Literature Watch
01-07-2013, 02:01 AM
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Replies: 25
Views: 9,113
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...
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Forum: Literature Watch
01-07-2013, 01:14 AM
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Replies: 25
Views: 9,113
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?...
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Forum: Bioinformatics
08-15-2012, 08:22 AM
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Replies: 4
Views: 3,012
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...
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Forum: Bioinformatics
08-10-2012, 01:49 AM
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Replies: 4
Views: 3,012
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...
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Forum: Illumina/Solexa
04-28-2012, 02:40 AM
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Replies: 6
Views: 4,346
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...
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Forum: Bioinformatics
04-27-2012, 03:14 AM
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Replies: 2
Views: 1,738
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Forum: Illumina/Solexa
04-27-2012, 03:04 AM
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Replies: 6
Views: 4,346
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Forum: Literature Watch
02-02-2012, 02:53 PM
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Replies: 25
Views: 9,113
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...
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Forum: Literature Watch
02-02-2012, 09:00 AM
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Replies: 25
Views: 9,113
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...
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Forum: Literature Watch
01-25-2012, 09:40 AM
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Replies: 25
Views: 9,113
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...
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Forum: General
01-23-2012, 01:07 PM
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Replies: 2
Views: 1,650
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...
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Forum: Literature Watch
01-18-2012, 07:35 AM
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Replies: 25
Views: 9,113
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Forum: Literature Watch
01-13-2012, 07:19 AM
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Replies: 25
Views: 9,113
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...
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Forum: Literature Watch
01-09-2012, 08:22 AM
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Replies: 25
Views: 9,113
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Forum: Literature Watch
01-09-2012, 02:20 AM
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Replies: 25
Views: 9,113
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...
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Forum: Literature Watch
01-06-2012, 09:20 AM
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Replies: 25
Views: 9,113
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...
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Forum: Literature Watch
01-06-2012, 08:58 AM
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Replies: 25
Views: 9,113
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...
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Forum: Illumina/Solexa
12-07-2011, 01:41 AM
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Replies: 4
Views: 5,533
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...
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Forum: Literature Watch
11-18-2011, 02:10 AM
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Replies: 25
Views: 9,113
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Forum: Bioinformatics
08-24-2011, 01:07 PM
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Replies: 2
Views: 2,790
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...
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Forum: General
08-24-2011, 08:48 AM
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Replies: 12
Views: 2,896
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Forum: General
08-24-2011, 08:33 AM
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Replies: 12
Views: 2,896
...
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...
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Forum: General
08-24-2011, 07:55 AM
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Replies: 12
Views: 2,896
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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