Hi, I want know about the basics of Downstream analysis of genome(DNA), tools used in it and applications. If you please suggest some papers , articles or sites where i can find what i'm looking for.
Thanks!
RJames
People sequence a genome for lots of reasons. For instance,
You are trying to assemble a genome for a previously unsequenced species.
You are interested in the frequency of alleles in a population containing several individuals
You are trying to figure out where certain chromatin-associated proteins (histones or transcription factors for instance) bind to DNA: ChIP-seq
You are interested in where chromatin-associated proteins DO NOT bind to DNA: FAIRE-seq, DNAse-seq
Your sequenced DNA is actually cDNA created via some RNA-seq experiment. A few things you might be trying to do: identify transcription start sites or analyse the transciptome throughout development or in response to changes in the environment
I can assure you that pages and pages can be written about every numbered statement I have made. Perhaps you can narrow down what you will be expected to do in a month to one of the things on my list.
I remember when I first started working in bioinformatics, I would get tasks where I was told our lab had some data and I just needed to 'analyze' it. So, if this is what happened for you, I sympathize. Unfortunately, good bioinformatics typically requires a lot more specificity. The first thing to do is define the biological question, then you can define the bioinformatic question.
You might want to talk with your PI/Boss about the research question he/she trying to answer.. See what you can do to answer the question.. For this you might want to understand more about the kind of data (DNA/RNA-seq/exomeetc.,) you have. See if you are trying to map your genomic data to a reference.. If so which reference sequence you want to use.. etc., The best thing to start with is talk with your team..
i think your question is too general. It's a bit like asking for a quick summary of the downstream analysis of radio signals. Genomic DNA is analysed in many ways. Roughly speaking sequencing machines give you chunks of DNA. You then either try and match them to known things, or reconstruct them. You might try to infer things about how much there is. Things to look up - mapping - variant calling - assembly The book on DNA analysis by Simon Tavare is a good place to get basic knowledge on genomes and how they are analysed, plus any of many online tutorials.
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Downstream analysis of what? please be specific
Its genomic DNA.
Tell us more about your data format, and what question you are trying to answer?
i just want to know the basics not specific. What is downsteam-anlysis? I have some single end ion torrent PGM 316 data in both fastaq and sff formats. I will start working on them within a month. i'm just collecting information and trying to know my field.
What biological question you are seeking an answer to? That would be helpful information.