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Search: Posts Made By: valeu
Forum: Bioinformatics 07-05-2017, 06:55 AM
Replies: 12
Views: 3,947
Posted By valeu
Does your new (tab-delimited) .bed file satisfy...

Does your new (tab-delimited) .bed file satisfy the requirements listed in the OncoCNV manual?

Check formats:
o reads should be given in .BAM format
o amplicon coordinates should be given in...
Forum: Literature Watch 09-22-2016, 02:16 AM
Replies: 76
Views: 29,823
Posted By valeu
Please send me the generated .cnp files and your...

Please send me the generated .cnp files and your config: valentina . boeva at inserm . fr
Valentina
Forum: Literature Watch 08-01-2016, 02:18 AM
Replies: 76
Views: 29,823
Posted By valeu
Hi, I do not see any evident mistake in the...

Hi, I do not see any evident mistake in the config file. If you want me to debug it, please share your config and corresponding files with me. Valentina.Boeva%at%inserm.fr
Forum: Academic/Non-Profit Jobs 06-27-2016, 01:56 AM
Replies: 0
Views: 415
Posted By valeu
Post-doctoral position in algorithms for cancer data analysis - Paris, France

Our group is looking for a post-doctoral researcher to develop methodology for the analysis of cancer epigenetics data (1 year project). We have already developed several widely used methods for...
Forum: Bioinformatics 04-25-2016, 02:39 AM
Replies: 12
Views: 3,947
Posted By valeu
I believe something is wrong with your .bed file...

I believe something is wrong with your .bed file with regions. Please check the readme.
Forum: Bioinformatics 08-26-2015, 05:48 AM
Replies: 12
Views: 3,947
Posted By valeu
For the test dataset, do you see that...

For the test dataset, do you see that './Test.stats.txt' has been created?

For the second dataset, I don't understand what is wrong.

Please, contact me by email.
Forum: Bioinformatics 02-10-2015, 09:30 AM
Replies: 12
Views: 3,947
Posted By valeu
ONCOCNV: a method to extract CNAs from amplicon (or targeted) sequencing data

We are happy to present ONCOCNV, a method to detect copy number alterations in amplicon or targeted sequencing data. The method can be applied to exome-seq data as well, but it will not adjust the...
Forum: Literature Watch 10-05-2014, 05:56 AM
Replies: 76
Views: 29,823
Posted By valeu
I will try to add it. But I assure you that the...

I will try to add it. But I assure you that the results will be the same as if you use hg18_snp130.SingleDiNucl.1based.txt
Forum: Literature Watch 09-23-2014, 09:43 AM
Replies: 76
Views: 29,823
Posted By valeu
FREEC uses overlapping windows to scan the genome...

FREEC uses overlapping windows to scan the genome (if step < window). This is why you may have overlapping predictions. The breakpoint should be located somewhere in the overlapping part.
Forum: Bioinformatics 08-27-2014, 01:27 AM
Replies: 9
Views: 2,676
Posted By valeu
GCcontentProfile should be a file with...

GCcontentProfile should be a file with GC-content per window (and not a value TRUE or FALSE). Just remove this line to create the GC-content profile using fasta files of your chromosomes.

Check...
Forum: Literature Watch 08-12-2014, 01:17 AM
Replies: 76
Views: 29,823
Posted By valeu
More variability in the normalized read count...

More variability in the normalized read count signal => less confidence in breakpoints.

Anyway, you can try and then visually check the resulting profile.
Forum: Literature Watch 08-11-2014, 02:32 PM
Replies: 76
Views: 29,823
Posted By valeu
I did not try, but I think with degree >3 the...

I did not try, but I think with degree >3 the result will be very similar to that with degree==3.

The ideal window size depends on read density. It is good to have about 400 reads per window....
Forum: Literature Watch 07-14-2014, 07:31 AM
Replies: 76
Views: 29,823
Posted By valeu
There is a problem with this SNP file. Please try...

There is a problem with this SNP file. Please try another one from the FREEC website.
Forum: Literature Watch 07-14-2014, 04:43 AM
Replies: 76
Views: 29,823
Posted By valeu
Hi, The config looks good. Could you please...

Hi,

The config looks good. Could you please share the complete output into the command line with me? [email protected]

Thank you
Valentina
Forum: Bioinformatics 01-09-2014, 12:16 AM
Replies: 9
Views: 2,676
Posted By valeu
I hope so :) But it is better to set step equal...

I hope so :)
But it is better to set step equal to window or to delete or comment it.
Forum: Bioinformatics 01-08-2014, 12:24 PM
Replies: 9
Views: 2,676
Posted By valeu
This can happen if step<window. You may use the...

This can happen if step<window. You may use the first coordinates of regions: in your case, 98600 and 122100.
Forum: Bioinformatics 12-18-2013, 08:27 AM
Replies: 9
Views: 2,676
Posted By valeu
Right, it does. The 5th column must...

Right, it does. The 5th column must "mappability". But if the 5th column is empty FREEC will use (1-poly(N)% as mappability.
Forum: Bioinformatics 09-26-2013, 06:46 AM
Replies: 7
Views: 3,690
Posted By valeu
Yes, you are right.

Yes, you are right.
Forum: Bioinformatics 09-25-2013, 03:27 AM
Replies: 7
Views: 3,690
Posted By valeu
No, so far there is such an option, although it...

No, so far there is such an option, although it could improve greatly the results. I think CONTRA does it in a right way. You can check. Otherwise, you can simple merge BAM files and use FREEC
Forum: Literature Watch 07-04-2013, 09:44 AM
Replies: 76
Views: 29,823
Posted By valeu
Both formats look correct. If you want me to...

Both formats look correct. If you want me to debug the code please send me an email with the config file, command line output and other files necessary to run FREEC.


If you disable [BAF] you...
Forum: Literature Watch 07-04-2013, 03:32 AM
Replies: 76
Views: 29,823
Posted By valeu
Hi, why don't you use the provided...

Hi, why don't you use the provided hg19_snp137.SingleDiNucl.1based.txt (created by Niklas Malmqvist)? Historically, the order of columns is different from the UCSC file.

To create my dbSNP files,...
Forum: Literature Watch 07-02-2013, 02:41 AM
Replies: 76
Views: 29,823
Posted By valeu
"Yes", if you don't use [BAF] and "No" if you do....

"Yes", if you don't use [BAF] and "No" if you do.



I would say that it is normal that you get different results. When you use [BAF], you use more information to (1) segment your data and (2) to...
Forum: Literature Watch 07-02-2013, 02:22 AM
Replies: 76
Views: 29,823
Posted By valeu
This is the latest version so far: makeGraph.R...

This is the latest version so far: makeGraph.R (http://xfer.curie.fr/get/6Am8msV3UKH/makeGraph.R)
Forum: Bioinformatics 06-06-2013, 10:46 AM
Replies: 7
Views: 3,690
Posted By valeu
Hi Jane, First, for CNV of the control...

Hi Jane,

First, for CNV of the control sample, I got a line at 2 for all my 25 patients (attached file "CNV.mpileup_normal_ratio.txt.png"). I wonder why there is no noise around 2 and why I cannot...
Forum: Literature Watch 01-19-2013, 08:15 AM
Replies: 76
Views: 29,823
Posted By valeu
No, mateOrientation is not relevant when you use...

No, mateOrientation is not relevant when you use pileup. Still, you need to set this parameter to something :)
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