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Search: Posts Made By: csoong
Forum: Bioinformatics 04-10-2011, 07:51 PM
Replies: 11
Views: 3,990
Posted By csoong
Luckily, dbSNP just released a fixed version in...

Luckily, dbSNP just released a fixed version in march (after I gone through all the hassle to get around the problem). They addressed the issue in the march release. I checked a few indel entries and...
Forum: Bioinformatics 03-06-2011, 05:08 AM
Replies: 24
Views: 7,178
Posted By csoong
the high through put sequencing technologies...

the high through put sequencing technologies might follow most other then-high-throughput technologies such as microarrays and that biology labs eventually would not have interest dealing with the...
Forum: Bioinformatics 03-05-2011, 02:12 AM
Replies: 24
Views: 7,178
Posted By csoong
with already 100M reads of 2*100bp from a single...

with already 100M reads of 2*100bp from a single hiseq lane, in house resources seem unlikely to catch up the amount of data increase. i vote for cloud solutions before any revolutionary computation...
Forum: Bioinformatics 02-25-2011, 12:32 PM
Replies: 0
Views: 1,958
Posted By csoong
dindel question

Hi all,

In the dindel manual there is a paragraph that reads:
Targeted resequencing: With targeted resequencing experiments, such as exome capture protocols, it is not possible to have reads on...
Forum: Bioinformatics 02-25-2011, 06:12 AM
Replies: 6
Views: 6,390
Posted By csoong
What did you mean by long rearrangements being...

What did you mean by long rearrangements being treated as short ones? I thought breakdancer outputs breakpoints info not about size of rearrangements. Could you clarify? I also agree with you, SV...
Forum: Bioinformatics 02-18-2011, 11:55 AM
Replies: 82
Views: 32,455
Posted By csoong
we could definitely DIY the process, the...

we could definitely DIY the process, the limitation being the bandwidth demand for any lab to do so. again this could be solved by using fedex-ing harddisks, but again who wants to take time in a lab...
Forum: Bioinformatics 02-17-2011, 12:01 PM
Replies: 14
Views: 3,481
Posted By csoong
thanks to all you people, i finally will have my...

thanks to all you people, i finally will have my hands on the files after speaking with the company
Forum: Bioinformatics 02-17-2011, 10:20 AM
Replies: 14
Views: 3,481
Posted By csoong
thats good to hear, at least now they can't say...

thats good to hear, at least now they can't say they arent giving out the bed files anymore

im using human sureselect all exon kit 50 mb
Forum: Bioinformatics 02-17-2011, 09:25 AM
Replies: 14
Views: 3,481
Posted By csoong
I don't know if others have run into problems of...

I don't know if others have run into problems of not being able to get a hand on commercialized exome baits bed files. I spoke with a sales rep and he told me it is proprietary info. yikes.
Forum: General 02-16-2011, 06:28 AM
Replies: 13
Views: 10,674
Posted By csoong
K, You are right about the RNA, but the bait...

K,
You are right about the RNA, but the bait design should be different. Nonetheless, it always bothered me when expression profiling involves amplification steps...
Wasn't there a protocol...
Forum: General 02-16-2011, 03:10 AM
Replies: 13
Views: 10,674
Posted By csoong
I would think with exome data there might be too...

I would think with exome data there might be too big a bias due to selection and pcr. A crude CNV info could be extracted though
Forum: Introductions 02-15-2011, 12:18 PM
Replies: 4
Views: 1,360
Posted By csoong
perhaps in summer

perhaps in summer
Forum: Bioinformatics 02-14-2011, 09:32 AM
Replies: 82
Views: 32,455
Posted By csoong
Another possibility to consider would be to only...

Another possibility to consider would be to only share certain variation files. But that is dependent on what defines variants and how variants are characterized and is sort of confined to DNA...
Forum: Bioinformatics 02-14-2011, 08:20 AM
Replies: 5
Views: 1,760
Posted By csoong
Never had any chip-seq experience. But are the...

Never had any chip-seq experience. But are the peaks directly related to coverage? since chip-seq only selects a portion of the genome having high coverage (hence seeing higher peaks) is expected,...
Forum: Bioinformatics 02-14-2011, 08:16 AM
Replies: 1
Views: 1,207
Posted By csoong
unfortunately John, there is no optimal...

unfortunately John, there is no optimal parameters it all depends on what you're looking for. it may sound crazy -- good luck!
Forum: Bioinformatics 02-14-2011, 07:23 AM
Replies: 3
Views: 2,314
Posted By csoong
I had no such problems in terms of not being able...

I had no such problems in terms of not being able to call longer indels.

For the overrepresentation of 1bp indel, maybe thats the true case. if you still don't believe Sanger sequence to verify...
Forum: Introductions 02-14-2011, 06:10 AM
Replies: 4
Views: 1,360
Posted By csoong
hi im from Taipei too

hi im from Taipei too
Forum: Bioinformatics 02-14-2011, 06:07 AM
Replies: 1
Views: 1,758
Posted By csoong
perhaps your reference genome was masked

perhaps your reference genome was masked
Forum: Illumina/Solexa 02-13-2011, 10:16 PM
Replies: 5
Views: 3,222
Posted By csoong
my guess is the elution buffer cause the DNA to...

my guess is the elution buffer cause the DNA to dissolve in solution instead of binding with the biotinylated baits. So AMPURE only purified the magnetic beads that contained the baits as you...
Forum: Illumina/Solexa 02-13-2011, 06:25 PM
Replies: 5
Views: 3,222
Posted By csoong
With Sureselect after the capture step there is a...

With Sureselect after the capture step there is a magentic streptavidin-biotin pull down I think that might be a step you had run trouble into (if Illumina also has a streptavidin-biotin pull...
Forum: Illumina/Solexa 02-13-2011, 12:17 PM
Replies: 5
Views: 3,222
Posted By csoong
I never worked with Illumina's exome kit (only...

I never worked with Illumina's exome kit (only Sureselect) but sounds like the capture step failed due to the elution buffer, the bait never binded with the DNA targets. Or if it did, the AMPURE step...
Forum: Bioinformatics 02-12-2011, 07:30 PM
Replies: 1
Views: 2,127
Posted By csoong
definitely, google IUPAC nucleotide codes and...

definitely, google IUPAC nucleotide codes and you'll find out
Forum: Literature Watch 02-12-2011, 03:53 AM
Replies: 5
Views: 2,626
Posted By csoong
I always felt curious about job security for...

I always felt curious about job security for bioinformaticians in a lab that does sequence analysis. First of all, it's not an industrial environment where programmers could be promoted to become...
Forum: Bioinformatics 02-11-2011, 06:14 PM
Replies: 17
Views: 7,673
Posted By csoong
Thanks for all the detailed responses! Could...

Thanks for all the detailed responses!
Could anyone further explain the difference of an early CCGG vs a late one? At the program level what is happening here?
Forum: Bioinformatics 02-11-2011, 03:58 AM
Replies: 2
Views: 2,913
Posted By csoong
according to your needs. if you got to dataset...

according to your needs. if you got to dataset being merged with different RG but are really the same you could modify it to become the same. if you got 2 dataset with same RG but actually different...
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