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