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Search: Posts Made By: KevinLam
Forum: Ion Torrent 01-25-2017, 04:35 PM
Replies: 4
Views: 2,682
Posted By KevinLam
Hi Alessandro, have you checked with your local...

Hi Alessandro, have you checked with your local tech support for Ion?

It takes a bit more work as the Torrent server is a virtual machine so by mounting it on your S5 doesn't automatically make...
Forum: Personalized Genomics 04-21-2016, 07:05 AM
Replies: 2
Views: 4,830
Posted By KevinLam
you need to order it through a physician though

you need to order it through a physician though
Forum: Bioinformatics 02-10-2016, 07:45 AM
Replies: 6
Views: 3,600
Posted By KevinLam
there's Personal Genome Project...

there's Personal Genome Project http://www.personalgenomes.org/harvard/data

curious what can be gleaned from the data...
Forum: Personalized Genomics 02-10-2016, 12:54 AM
Replies: 3
Views: 6,764
Posted By KevinLam
2 years after they are still on microarray...

2 years after they are still on microarray although they keep changing their array design
Forum: Bioinformatics 09-27-2015, 08:19 PM
Replies: 18
Views: 15,663
Posted By KevinLam
https://github.com/DecodeGenetics/BamHash is...

https://github.com/DecodeGenetics/BamHash
is this the bamhash you are referring to?
I wonder how fast it is ...

http://www.html5rocks.com/en/tutorials/speed/txt-compression/ there's a hint in...
Forum: Clinical Sequencing 09-30-2014, 07:28 PM
Replies: 1
Views: 6,889
Posted By KevinLam
Can't see where it says $729 on their website ......

Can't see where it says $729 on their website ... what does it cover?
Forum: Clinical Sequencing 09-30-2014, 07:18 PM
Replies: 1
Views: 6,411
Posted By KevinLam
But they do sell you the compute server...

But they do sell you the compute server separately when you purchase the PGM yes?
I have not heard about the Ingenuity pipeline but am interested to know more. for clinical diagnostics
the fact...
Forum: General 09-30-2014, 07:10 PM
Replies: 1
Views: 881
Posted By KevinLam
where to find refurbished HiSeq2000?

Anyone knows how I might get my hands on one? Where do they go after Illumina acquires them for trade in programs? I would prefer to work with a company based in South East Asia if that's possible
Forum: Illumina/Solexa 07-26-2013, 12:18 AM
Replies: 31
Views: 15,477
Posted By KevinLam
they have 3000 8.5 kb reads now .. and it's avail...

they have 3000 8.5 kb reads now .. and it's avail as a public dataset more details here
http://kevin-gattaca.blogspot.sg/2013/07/what-would-you-do-with-3k-of-8500-bp.html

Done a FASTQC on both...
Forum: Bioinformatics 11-06-2012, 06:10 AM
Replies: 11
Views: 3,478
Posted By KevinLam
hmm is your problem related to the thread...

hmm is your problem related to the thread starter's?

else you could possibly see if galaxy already has the data else upload via the ftp link then extract the portion you want via the UCSC link on...
Forum: Bioinformatics 08-21-2012, 12:53 AM
Replies: 4
Views: 2,344
Posted By KevinLam
one good reason you wanna sort/index your bam ...

one good reason you wanna sort/index your bam
is so that you can split your bams into chr or even regions so that you can parallelize your mpileup calls.
Forum: Personalized Genomics 06-12-2012, 11:45 AM
Replies: 8
Views: 7,556
Posted By KevinLam
saw a presentation from Bioteam/ british telecom ...

saw a presentation from Bioteam/ british telecom
so they managed to do a POC with Siri voice activated questions that starts cloud analysis of your data ...
admittedly the potential for real time...
Forum: Bioinformatics 06-12-2012, 11:20 AM
Replies: 3
Views: 1,760
Posted By KevinLam
Broad best practices workflow in Galaxy

I read about some users trying to recreate the Broad's workflow for SNPs within a local galaxy install. Did anyone have success with it?
How might I do this with the least amount of effort?

are...
Forum: Bioinformatics 06-12-2012, 11:17 AM
Replies: 1
Views: 1,227
Posted By KevinLam
Best way to realign / test other aligners with bams generated with casava

Hi
Long story short. Only got bams from casava (and misc other bams and files BUT no fastq) from seq provider ...
I actually wish to use Broad's best practices workflow on the data.

What are...
Forum: Ion Torrent 05-17-2012, 07:43 AM
Replies: 9
Views: 7,367
Posted By KevinLam
I never thought I would live to see 'sour grapes'...

I never thought I would live to see 'sour grapes' as a tag in a post here. :D

To be fair, I do not think platform bias should surprise anyone. Perhaps the knee jerk reaction is that PGM isn't...
Forum: Bioinformatics 04-12-2012, 11:34 PM
Replies: 3
Views: 1,866
Posted By KevinLam
hmm double posting here ...

hmm double posting here
http://seqanswers.com/forums/showthread.php?t=19156
to TS I think it's more helpful to have all comments on a single thread yeah?
Forum: Bioinformatics 01-03-2012, 06:07 AM
Replies: 6
Views: 3,025
Posted By KevinLam
U can consider running alightment of split fastq...

U can consider running alightment of split fastq files before merging bam files .. If upload is slow
Forum: Illumina/Solexa 12-11-2011, 11:47 PM
Replies: 4
Views: 4,856
Posted By KevinLam
out of curiousity, your illumina reads are from...

out of curiousity, your illumina reads are from GAIIx? or HiSeq? AFAIK, differences in the sample prep resulted in a different GC coverage profile even within the same companies' platform. ...
Forum: Genomic Resequencing 11-22-2011, 04:53 PM
Replies: 0
Views: 6,074
Posted By KevinLam
wet lab Validation of a large number of SNPs

Hi
AFAIK
you can validate SNPs obtained by Hi-seq by
microarray,
Sanger Seq,
NGS seq on a different platform

Which are the more common / cost effective approach for a large number of...
Forum: Bioinformatics 11-15-2011, 10:57 PM
Replies: 28
Views: 57,059
Posted By KevinLam
On Picard, my service provider mentioned this ...

On Picard,
my service provider mentioned this
"Using picard tools directly has one significant drawback. Picard tools will read in sequence from the BAM
line by line and cache it until it has...
Forum: Ion Torrent 08-23-2011, 08:13 PM
Replies: 14
Views: 9,112
Posted By KevinLam
www.aitbiotech.com is an Ion Torrent service...

www.aitbiotech.com is an Ion Torrent service provider in asiapac region
Forum: SOLiD 08-02-2011, 11:33 PM
Replies: 5
Views: 2,904
Posted By KevinLam
have you tried fastqc? ...

have you tried fastqc?

http://hts.rutgers.edu/filter/ is also useful in assessing QV distribution
Forum: SOLiD 04-30-2011, 03:08 AM
Replies: 5
Views: 1,792
Posted By KevinLam
you do mean that you counted the mapped and...

you do mean that you counted the mapped and unmapped files? and the numbers do not add up?
which version of Bioscope are you using? can you post the ini file?
Forum: Ion Torrent 04-25-2011, 12:19 AM
Replies: 7
Views: 4,715
Posted By KevinLam
Is there a direct link to download Tmap for a...

Is there a direct link to download Tmap for a test drive?

Had a hard time finding the torrent dev link
and then i had to register to enter.

here's direct link for benefit of others...
Forum: Ion Torrent 04-25-2011, 12:05 AM
Replies: 10
Views: 4,644
Posted By KevinLam
OMG this had better be not from LIFE ... oh...

OMG this had better be not from LIFE ...
oh wait it is... hmmm

Definitely worth a watch!
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