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Search: Posts Made By: wuhoucdc
Forum: Bioinformatics 08-27-2010, 03:47 PM
Replies: 147
Views: 44,510
Posted By wuhoucdc
Hi Kai, Can Pintel call large structural...

Hi Kai,

Can Pintel call large structural variants (>1M) now?

Thanks.

Wu
Forum: Bioinformatics 08-25-2010, 10:35 AM
Replies: 1
Views: 1,118
Posted By wuhoucdc
Samtool Pileup file

Hello All,

Have you seen a pileup file like this?
chr1 862 N G 4 0 3 1 ^$G 8
chr1 863 N C 4 0 3 1 C ...
Forum: Bioinformatics 08-24-2010, 08:41 PM
Replies: 15
Views: 5,739
Posted By wuhoucdc
Hi, You could try SVA in DUKE...

Hi,

You could try SVA in DUKE (http://people.genome.duke.edu/~dg48/sva/index.php).

I think this big guy can satisfy your request if you have a big computer.

Wu
Forum: Bioinformatics 08-24-2010, 07:24 PM
Replies: 12
Views: 9,716
Posted By wuhoucdc
Hi ruping, So that means I can not convert...

Hi ruping,

So that means I can not convert large sam files into bam?[/QUOTE]


I think you can convert sam files as large as possible to bam. I have tried a sam file more than 100G.

Wu
Forum: Bioinformatics 08-22-2010, 04:06 PM
Replies: 292
Views: 139,961
Posted By wuhoucdc
Dear All, Do you know if samtools can...

Dear All,

Do you know if samtools can perform multiple commands (>2) together? Here assuming that I have ten BAM files (result001.bam, result002.bam,......result010.bam) and want to merge them...
Forum: Bioinformatics 08-22-2010, 01:16 PM
Replies: 3
Views: 1,859
Posted By wuhoucdc
Thanks for your answer, dawe. But why did...

Thanks for your answer, dawe.

But why did you say "Never had a whole genome with that coverage "? Most of the sequenced individuals such as YH (PMID:18987735) and AK1 (PMID:19587683) were higher...
Forum: Bioinformatics 08-21-2010, 08:45 PM
Replies: 3
Views: 1,859
Posted By wuhoucdc
Transfer a whole genome with .bam format

Dear all,

Do you have experience to transfer a whole genome of short-reads with ~35X sequenced by Illumina GA to .bam format using samtools? I feel very strange when I got more than 500G data. I...
Forum: Bioinformatics 02-16-2010, 08:22 PM
Replies: 292
Views: 139,961
Posted By wuhoucdc
Hi lh3, Does SAMtools call SV currently?...

Hi lh3,

Does SAMtools call SV currently? Thanks

Wuhoucdc
Forum: Bioinformatics 02-13-2010, 11:46 AM
Replies: 16
Views: 4,425
Posted By wuhoucdc
Thanks a lot for the good package, Dongliang....

Thanks a lot for the good package, Dongliang. I'll try it in my data.
Forum: Bioinformatics 11-13-2009, 10:30 AM
Replies: 236
Views: 504,051
Posted By wuhoucdc
Thanks ECO for your kind suggestions. ...

Thanks ECO for your kind suggestions.

Wuhoucdc
Forum: Bioinformatics 11-13-2009, 08:10 AM
Replies: 236
Views: 504,051
Posted By wuhoucdc
Hi all, Who have the time to summarize the...

Hi all,

Who have the time to summarize the programs that can be used call SV such as large rearrangement, deletion, amplication among NGS? Thanks.

Wuhoucdc
Forum: Literature Watch 11-12-2009, 09:11 AM
Replies: 2
Views: 3,723
Posted By wuhoucdc
Hi Dione, After read more carefully on your...

Hi Dione,

After read more carefully on your website about this new technology, I think it will be applied rapidly on various domains. I hope this technology will bring us new chance among human...
Forum: Literature Watch 11-11-2009, 01:05 PM
Replies: 2
Views: 3,723
Posted By wuhoucdc
The so-call third-generation sequencing coming, but is it credible?

Hi all,

I just read the following paper named Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays from Science Express. In this paper, a sequencing corporation,...
Forum: Bioinformatics 11-05-2009, 09:32 PM
Replies: 236
Views: 504,051
Posted By wuhoucdc
Thanks Sci_guy pasted such a great resource!

Thanks Sci_guy pasted such a great resource!
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