Downstream Analysis
2
0
Entering edit mode
9.4 years ago

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

• 10k views
ADD COMMENT
2
Entering edit mode

Downstream analysis of what? please be specific

ADD REPLY
0
Entering edit mode

Its genomic DNA.

ADD REPLY
1
Entering edit mode

Tell us more about your data format, and what question you are trying to answer?

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
2
Entering edit mode

What biological question you are seeking an answer to? That would be helpful information.

ADD REPLY
5
Entering edit mode
9.4 years ago
KCC ★ 4.0k

People sequence a genome for lots of reasons. For instance,

  1. You are trying to assemble a genome for a previously unsequenced species.

  2. You are interested in the frequency of alleles in a population containing several individuals

  3. You are trying to figure out where certain chromatin-associated proteins (histones or transcription factors for instance) bind to DNA: ChIP-seq

  4. You are interested in where chromatin-associated proteins DO NOT bind to DNA: FAIRE-seq, DNAse-seq

  5. 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.

ADD COMMENT
0
Entering edit mode

yes its something like that. I don't have any idea where the the originated. i was just told that i will be doing analysis of the said data.

ADD REPLY
0
Entering edit mode

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..

ADD REPLY
0
Entering edit mode

@George: Great answer for a beginner to think about and little googling would help @rjames.biotech..

ADD REPLY
2
Entering edit mode
9.4 years ago

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.

ADD COMMENT

Login before adding your answer.

Traffic: 2282 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6