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Search: Posts Made By: vasvale
Forum: Clinical Sequencing 01-08-2016, 03:17 PM
Replies: 4
Views: 4,392
Posted By vasvale
I am looking for average in human genomes, could...

I am looking for average in human genomes, could not find info on exomes papers
Forum: Clinical Sequencing 01-08-2016, 08:56 AM
Replies: 4
Views: 4,392
Posted By vasvale
How many missense/nonsense per coding Mb?

what is average number of missense/nonsense per Mb of coding DNA? I found 500 variants/Mb but that includes also synonimous.
Forum: Bioinformatics 01-07-2016, 03:46 PM
Replies: 0
Views: 928
Posted By vasvale
How many missense/nonsense per coding Mb?

what is average number of missense/nonsense per Mb of coding DNA? I found 500 variants/Mb but that includes also synonimous.
Forum: Bioinformatics 07-30-2012, 02:04 PM
Replies: 2
Views: 1,739
Posted By vasvale
annotated exons

is there any update on this also based on rna-seq data?
Forum: Sample Prep / Library Generation 08-07-2011, 09:55 AM
Replies: 3
Views: 2,372
Posted By vasvale
I usually load the flow cell for a GAIIx run at 9...

I usually load the flow cell for a GAIIx run at 9 pM.
Forum: Sample Prep / Library Generation 08-07-2011, 09:54 AM
Replies: 3
Views: 2,372
Posted By vasvale
ssDNA in sample from targeted exon capture affecting quantification

Has anybody experienced this problem:?

I had too many clusters in a run and I’d like to ask if it ever happened to you: the DNA samples may have some single stranded DNA that is not quantified by...
Forum: Sample Prep / Library Generation 08-07-2011, 09:52 AM
Replies: 2
Views: 8,748
Posted By vasvale
nextera for targeted exon capture?

is nextera library prep OK to do exon capture?
Forum: Sample Prep / Library Generation 08-07-2011, 09:50 AM
Replies: 14
Views: 54,691
Posted By vasvale
salt composition

may check with Agilent about effects of sample's salt/tween that change the migration
Forum: Bioinformatics 11-15-2010, 08:35 AM
Replies: 4
Views: 2,188
Posted By vasvale
best tool for indels?

hello

we have a sample with a 10 bases deletion and 2 nt insertion that is not detected with the following tools: eland-extended+Casava/bwa-gatk/bfast

any suggestion on what else to try?
...
Forum: Illumina/Solexa 08-30-2010, 04:48 PM
Replies: 24
Views: 26,833
Posted By vasvale
hello as some time has past since the last...

hello

as some time has past since the last posting I wonder if anybody has an improved method for indexing for single-reads

Vasvale
Forum: Illumina/Solexa 10-16-2009, 09:32 AM
Replies: 15
Views: 6,764
Posted By vasvale
I'd need it for single-end reads for genomic DNA ...

I'd need it for single-end reads for genomic DNA
don't know how to use MAQ
Forum: The Pipeline 10-06-2009, 02:10 PM
Replies: 5
Views: 5,213
Posted By vasvale
yeld

so one run produces 70 gbp andf 70 bp reads?
Forum: Bioinformatics 09-18-2009, 09:37 AM
Replies: 1
Views: 1,322
Posted By vasvale
also any comparison btw Casava/ DNAstar/Nextgene?

also any comparison btw Casava/ DNAstar/Nextgene?
Forum: Literature Watch 09-17-2009, 05:51 PM
Replies: 0
Views: 1,671
Posted By vasvale
Methods for genomic partitioning.

Annu Rev Genomics Hum Genet. 2009;10:263-84.

Methods for genomic partitioning.

Turner EH, Ng SB, Nickerson DA, Shendure J.
Forum: Literature Watch 09-17-2009, 05:50 PM
Replies: 0
Views: 1,524
Posted By vasvale
12 human exomes

Ng SB, Turner EH, Robertson PD, Flygare SD, Bigham AW, Lee C, Shaffer T, Wong
M, Bhattacharjee A, Eichler EE, Bamshad M, Nickerson DA, Shendure J. Targeted
capture and massively parallel...
Forum: Bioinformatics 09-17-2009, 05:43 PM
Replies: 19
Views: 27,038
Posted By vasvale
duplicate reads removal

is there any software that removes duplicate single-reads? (Casava does it for paired-end reads only)
Forum: Bioinformatics 09-17-2009, 05:42 PM
Replies: 1
Views: 1,322
Posted By vasvale
Maq v Pipeline

has anybody compared the output of Maq and Pipeline interms of variants detected?
Forum: Illumina/Solexa 09-17-2009, 05:37 PM
Replies: 15
Views: 6,764
Posted By vasvale
Casava does it only for paired-end reads it...

Casava does it only for paired-end reads

it is very important to do it also for single reads but it is not provided by Illumina
if you don't remove repeated reads you'll get more errors (see ...
Forum: Illumina/Solexa 04-20-2009, 11:33 AM
Replies: 13
Views: 2,501
Posted By vasvale
would it be possible to have some details about...

would it be possible to have some details about how you do long range PCR and barcoding? I noticed that there are so many polymorphisms that it seems hard to design primers in conserved regions
...
Forum: Illumina/Solexa 04-17-2009, 08:01 AM
Replies: 13
Views: 2,501
Posted By vasvale
mtDNA

Thank you, my question is about the upstream phase of the experiments, do you enrich by PCR pr long range PCR? can you append barcodes?

thanks

Vasvale
Forum: Illumina/Solexa 04-15-2009, 06:05 PM
Replies: 13
Views: 2,501
Posted By vasvale
mitochondria

Hello

can you kindly let me know how you proceed to seq mtDNA? are there papers?
thanks

Vasvale
Forum: Sample Prep / Library Generation 01-27-2009, 09:31 AM
Replies: 0
Views: 1,990
Posted By vasvale
hybridization platform

Hello

has anybody used the Nimblegen hyb platform and elution station with Agilent arrays?

Thanks

Vasvale

this paper has new improvements for library prep
Forum: 454 Pyrosequencing 01-27-2009, 09:23 AM
Replies: 61
Views: 74,802
Posted By vasvale
imp[rovements for the library prep in this paper:...

imp[rovements for the library prep in this paper:
Nat Methods. 2008 Dec;5(12):1005-10.

A large genome center's improvements to the Illumina sequencing system.

Quail MA, Kozarewa I, Smith F,...
Forum: Sample Prep / Library Generation 11-16-2008, 04:27 PM
Replies: 29
Views: 25,121
Posted By vasvale
could you please explain what is the near target...

could you please explain what is the near target problem? txs
Forum: 454 Pyrosequencing 11-11-2008, 04:26 PM
Replies: 9
Views: 7,432
Posted By vasvale
below is a reference for the PCR error, can...

below is a reference for the PCR error, can somebody eplain why homopolymers error are seen with Roche and not with other platforms (as I heard)

Clarke LA, Rebelo CS, Gonçalves J, Boavida MG,...
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