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Search: Posts Made By: KevinLam
Forum: Ion Torrent 11-02-2020, 08:53 AM
Replies: 1
Views: 5,366
Posted By KevinLam
soft clipped means they are not used? what do you...

soft clipped means they are not used? what do you hope to achieve by removing them?
Forum: Ion Torrent 11-02-2020, 08:41 AM
Replies: 1
Views: 3,052
Posted By KevinLam
Yes the fastq is generated from the bam file...

Yes the fastq is generated from the bam file which is
low quality trimmed
barcode and adaptor trimmed
Forum: Ion Torrent 11-02-2020, 08:34 AM
Replies: 2
Views: 1,990
Posted By KevinLam
Hmm NIPT data would be clinical data no? That...

Hmm NIPT data would be clinical data no? That might represent some difficulty without prior consent
Forum: Ion Torrent 11-02-2020, 08:28 AM
Replies: 4
Views: 616
Posted By KevinLam
I would have pointed you to...

I would have pointed you to http://seqanswers.com/forums/showthread.php?t=62920 but I think it's better to look towards the future (not sure if PGM is still being sold) and you really should just...
Forum: Service Providers 08-04-2020, 10:47 PM
Replies: 1
Views: 1,877
Posted By KevinLam
Hmm e-dna? environmental DNA? deep...

Hmm e-dna?
environmental DNA?
deep metagenomics?

I think Ion Torrent does a fairly good job of this ..
Forum: Ion Torrent 01-20-2020, 07:07 AM
Replies: 1
Views: 2,162
Posted By KevinLam
Have you tried checking with Premaitha?

Have you tried checking with Premaitha?
Forum: Ion Torrent 01-25-2017, 05:35 PM
Replies: 4
Views: 3,089
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, 08:05 AM
Replies: 2
Views: 6,756
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, 08:45 AM
Replies: 6
Views: 4,059
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, 01:54 AM
Replies: 3
Views: 8,836
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, 09:19 PM
Replies: 18
Views: 18,333
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, 08:28 PM
Replies: 1
Views: 8,873
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, 08:18 PM
Replies: 1
Views: 8,305
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, 08:10 PM
Replies: 1
Views: 1,051
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, 01:18 AM
Replies: 31
Views: 16,841
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, 07:10 AM
Replies: 11
Views: 3,922
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, 01:53 AM
Replies: 4
Views: 2,902
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, 12:45 PM
Replies: 8
Views: 9,779
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, 12:20 PM
Replies: 3
Views: 2,043
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, 12:17 PM
Replies: 1
Views: 1,438
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, 08:43 AM
Replies: 9
Views: 8,081
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 04-13-2012, 12:34 AM
Replies: 3
Views: 2,266
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, 07:07 AM
Replies: 6
Views: 3,301
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 12-12-2011, 12:47 AM
Replies: 4
Views: 5,434
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, 05:53 PM
Replies: 0
Views: 6,361
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...
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