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Forum: Bioinformatics 12-28-2014, 11:47 PM
Replies: 2
Views: 1,740
Posted By southan
You can also use CNVrd2: ...

You can also use CNVrd2:

http://www.bioconductor.org/packages/devel/bioc/html/CNVrd2.html
Forum: Bioinformatics 05-07-2014, 07:46 PM
Replies: 4
Views: 1,637
Posted By southan
You can use the Mclust package. ...

You can use the Mclust package.

(http://www.stat.washington.edu/mclust/)

Change the parameter modelNames to obtain a suitable model (e.g., EII).
Forum: Bioinformatics 05-06-2014, 04:04 PM
Replies: 0
Views: 754
Posted By southan
Pindel for multiple samples (cannot see large variants)

Hi all!

I'm using Pindel to analyse 200 samples on a small region.

When I ran for single samples, it was OK and I could see variants > 70 kb.

However, it did not report these variants when...
Forum: Bioinformatics 12-21-2013, 09:31 PM
Replies: 1
Views: 2,612
Posted By southan
You can use dwgsim...

You can use dwgsim http://sourceforge.net/apps/mediawiki/dnaa/index.php?title=Whole_Genome_Simulation

On their website, they explain how to use it.
Forum: Bioinformatics 02-25-2013, 06:44 PM
Replies: 37
Views: 87,232
Posted By southan
I'm going to download Bam files from the Project....

I'm going to download Bam files from the Project.
I see two links:
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/
and
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/

There are some...
Forum: Bioinformatics 06-27-2011, 03:00 AM
Replies: 4
Views: 1,866
Posted By southan
Thank Laura, It's Ok now. I used: 1/...

Thank Laura,

It's Ok now.

I used:
1/ tabix to get some regions from chr1.
2/ Vcf-subset to get samples from the regions.
Forum: Bioinformatics 06-26-2011, 03:54 PM
Replies: 4
Views: 1,866
Posted By southan
Thank Laura! I downloaded one chromosome of...

Thank Laura!

I downloaded one chromosome of SNPs on the website.

I am using VCFtools to extract individuals but it takes a lot of time to get each individuals (22 samples in two days).

Do...
Forum: Bioinformatics 06-13-2011, 07:38 PM
Replies: 39
Views: 15,500
Posted By southan
cnvnator -root NA18507.root -view 100 ...

cnvnator -root NA18507.root -view 100

That's Ok.
Are you using ssh? If so, you should use ssh -X.
Forum: Bioinformatics 06-13-2011, 12:46 AM
Replies: 4
Views: 1,866
Posted By southan
Using dbsnps or use samtools to call from 1000 genomes

Hi all,

I am going to get snps in chr1 on 1000 genomes (latest).
Do you think I should use dbsnp132 or I should use samtools to call snps again from bam files on 1000 genomes?

Thank you very...
Forum: Bioinformatics 06-12-2011, 06:36 PM
Replies: 39
Views: 15,500
Posted By southan
I use this line: source...

I use this line:
source /path/root/bin/thisroot.sh
Forum: Bioinformatics 05-10-2011, 05:00 PM
Replies: 39
Views: 15,500
Posted By southan
Before you use cnvnator, you can go to (or not)...

Before you use cnvnator, you can go to (or not) "root/bin/" and type this line:
source thisroot.sh
It will automatically set your ROOTSYS.
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