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Hello everybody,
I'm not a professional bioinformatician, but just a Java developer here in Luxembourg with a long-standing interest in the field. As such, I'm on a mission to learn some bioinoformatics skills, and understand a few things about my own genome while I'm at it. To this end, I've obtained (for $1300), my own complete exome, as well as BAM and VCF files, from GeneByGene. If anybody has any experiences to share about this company (good or bad), I'd be very interested to hear them. Personally, I can say that, while the processing took a very long time, they did come through, and I'm not disappointed.
So...
After much struggling with various tools, I finally managed to open the BAM file. I am using Ugene and the Integrated Genome Browser. I've managed to locate the infamous SLC6A4 (AKA 5-HTTLPR) gene in my own genome. My next goal will be to determine which of the 14-or-so alleles I have. To achieve this, I have been searching all over the internet for an allele database, but all I've found is a the Immuno Polymorphism Database (http://www.ebi.ac.uk/ ), which seems mainly focused on genes controlling the immune system. In any case, I can't make any sense of the nomenclature in this database, so I can't find my SLC6A4 genes.
What am I doing wrong? Can somebody please point me to a resource where I can find all alleles (not just SNPs) for a specific gene?
Also, being a neophyte here, I have general question about FASTA files. Each chromosome exists as a pair, but in the human reference genome (and my own BAM), I see each chromosome as just a single strand of nucleotides. Is the pair just mixed together in some way? Is there no way to separate the two chromosomes?
Thanks in advance, and apologies for my general ignorance here.
Marc
I'm not a professional bioinformatician, but just a Java developer here in Luxembourg with a long-standing interest in the field. As such, I'm on a mission to learn some bioinoformatics skills, and understand a few things about my own genome while I'm at it. To this end, I've obtained (for $1300), my own complete exome, as well as BAM and VCF files, from GeneByGene. If anybody has any experiences to share about this company (good or bad), I'd be very interested to hear them. Personally, I can say that, while the processing took a very long time, they did come through, and I'm not disappointed.
So...
After much struggling with various tools, I finally managed to open the BAM file. I am using Ugene and the Integrated Genome Browser. I've managed to locate the infamous SLC6A4 (AKA 5-HTTLPR) gene in my own genome. My next goal will be to determine which of the 14-or-so alleles I have. To achieve this, I have been searching all over the internet for an allele database, but all I've found is a the Immuno Polymorphism Database (http://www.ebi.ac.uk/ ), which seems mainly focused on genes controlling the immune system. In any case, I can't make any sense of the nomenclature in this database, so I can't find my SLC6A4 genes.
What am I doing wrong? Can somebody please point me to a resource where I can find all alleles (not just SNPs) for a specific gene?
Also, being a neophyte here, I have general question about FASTA files. Each chromosome exists as a pair, but in the human reference genome (and my own BAM), I see each chromosome as just a single strand of nucleotides. Is the pair just mixed together in some way? Is there no way to separate the two chromosomes?
Thanks in advance, and apologies for my general ignorance here.
Marc
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