Tagged Questions
2
votes
0answers
27 views
What does conditional analysis of a SNP in a GWA study entail?
I am familiar with the use of tag-SNPs in genome-wide association studies to identify gene loci involved in complex traits, but I keep seeing the term "conditional analysis" used without any ...
4
votes
2answers
67 views
Combining gene expression data from two species
I currently have two sets of gene expression data. The first is a dataframe of genes identified by Annotation id CG numbers (for example "CG10005") in one column and a numerical variable of interest ...
4
votes
1answer
82 views
Can forensic DNA analysis be used to generate a visual approximation of a suspect?
In light of the current US supreme court case, I'm curious if enough information can be teased out of a DNA sample to get a "reasonable" approximation of the suspect (never mind the legality). I ...
1
vote
1answer
57 views
What is the best way to read and normalize large amounts of Agilent data into R? [closed]
I have a large amount of Agilent data (580 text files that are ~200 MB in size each) that I'd like to normalize. I've run into a problem in that my machine (with 8 GB of memory) still runs out of ...
3
votes
1answer
47 views
Is copy number variation dynamic?
Is there any evidence showing that copy number variation changes over time? I'm wanting to model interactions in expression level as a dynamic bayesian network, but an assumption my approach will need ...
4
votes
1answer
87 views
Which way to run BLAST?
I have a set of scaffolds from a genome assembly, and I want to align a collection of proteins from various species to it. I can do this using BLAST in two ways:
Create a BLAST database of the ...
6
votes
1answer
163 views
Does DNA contain information beyond protein synthesis?
It's well known that genetic information is stored in DNA. As far as I know, DNA only has information at the protein level. What about higher levels, such as organelles, cells, tissue, organs? Is ...
2
votes
2answers
60 views
Microbiome Data
How is it possible to access microbiome data like that found here? I'd like to perform analyses on similar type of data, but cannot find OTU data like that at the Human Biome Project. Thanks for any ...
5
votes
1answer
77 views
Assembly of metagenomic data
I'm trying to assemble metagenomic data that comes from termite guts. The sequences comes from SOLiD and no paired, so the reads are extremely short (25bp).
I have tried multiple assemblers (CLC, ...
9
votes
2answers
141 views
Shortest strings not present in the human genome
What length are the shortest strings of DNA not present in any known person's genome, and what are they?
And is there a database online by which I could find this out?
11
votes
4answers
192 views
Why did high A+T content create problems for the Plasmoduim falciparum genome project?
The main paper for the Plasmodium palciparum genome project (Gardner et al., 2002) repeatedly mentioned that the unusually high A+T content (~80%) of the genome caused problems. For example they imply ...
2
votes
0answers
111 views
Too few transcripts from transcriptome assembler Oases
I am trying to run Oases for transcriptome assembly. The result is far from expected, so I would like to ask whether I am running it in a right way? Thanks.
Here is my running command:
...
10
votes
4answers
192 views
What can you tell about a person, having only their whole genome as information?
Well, the question is in the title, no explanation need.
