[hdchen]

Hi everyone, I am Haodong from UCLA. I'm a second year graduate student.

[yclin]

Hi from yclin

Hi everyone,

Happy to find here.

I'm a grad student in Illinois, US and just start working on RNA-Seq data of Illumina or 454.

Best Regards

[Anri]

Hi from Estonia

I'm Anri, graduate student from Tallinn. Have been working with phage display for some time and now I'm trying to mix it with some Illumina/Solexa in order to get most out of it.

[shu]

hey all,
was wondering if anyone has worked with the CASAVA1.6 build..??
kinda stuck trying to generate genome studio tracks/inputs from aligned matepair data..
any help is appreciated..
thanks
best
shu

[Joe2]

Yello !

Hi Everyone,

I'm a research assistant (bioinformatics) looking for SNPs. Have you seen them ?

Actually we are currently looking at all our options for setting up a data analysis pipeline for dicovering SNPs (mainly from SOLiD data). We are looking at a number of cancers and hoping to find novel mutations (not in dbSNP) for further investigation. Any help will be appreciated and in a little while I hope i'll be able to give some answers myself....

good to meet you's,

Joe

[shu]

hey joe,
nice to meet you too and thanks for your reply..We did manage to fire CASAVA .. and we do observe a lot of snps.. Obviously we have to filter out and land on those precious few.. dbsnp-ve somatic snps.. do you use any particular algorithm for SNP validation prior to experimental validation?? I have heard of SIFT..was wondering if there are any better.. SIFT is mainly for exonic snps..

[Joe2]

Sorry Shu we havnt got any such algorithm working yet. but this is from the SOAPsnp site;

"SOAPsnp uses a method based on Bayes’ theorem (the reverse probability model) to call consensus genotype by carefully considering the data quality, alignment, and recurring experimental errors."

We are also looking at doing some more filtering in MySQL if neccessary.

[Vladimir]

Good evening, everyone, I'm writing you from EMBL Genomics Core Facility in Heidelberg, Germany, of which I'm in charge. We've got 3 GAIIx, which we like, more or less. We are running pretty much every imaginable application on them and mostly successfully, luckily. However, the devil is in the detail and thus we also have gone thru our share of rather frustrating moments coming from all possible corners of GAIIx space.
Cheers, Vladimir

[mkeehan]

Gidday,

My name is Mike, I work for LIC, a dairy breeding cooperative in Hamilton, New Zealand. We use sequence data to breed better dairy bulls for pastoral based dairy farmers throughout the world.

"Our mice are large, black and white."

[shu]

SIFT reaches the ceiling when it comes to het(1/2) called SNPs.. any obivous ways(computational) to get around it??not so obvious ones will be appreciated as well..

[hironobu]

Hello, everybody,

I am working in Japan. Just I started working with illumina GAIIx for EST and RNA sequencing.

Best wishes!

[tatinhawk]

Hi My Name is Martin I'm an Undergrad Student at the National Autonomous University of Mexico (UNAM), I'm a student in the undergrad program of Genomic Sciences . Nowadays I'm working with solexa reads for my research project.

[BearClaw]

I'm a Research Biologist working at Merck Research Laboratories. I'm pretty new to next-gen sequencing but not new to most of the bench techniques. I've already gotten a couple of good suggestions off this forum! I hope to be able to help in the future as much as I get help now.

[Bruins]

Hi,

Am undergrad student working at UMC Groningen, the Netherlands. Today is my first day and I'll be using Taverna to set up a pipeline for Genome Analyzer data analysis.

Cheers!

[isharon]

Hello everyone!

I am a PhD student at the Technion, Israel Institute of Technology. Usually working on metagenomics, but in the coming few months will be working on Solexa data.

Cheers,
Itai