The study of genomes, the entire set of genes in an organism.

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2answers
68 views

How much genomic variation one usually find within a given bacterial species?

If I find the exact starting position (say 1152471) of the coding sequence of a given gene in the genome of a bacterium, is the genome of the bacterium in general stable enough so that I can expect to ...
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1answer
18 views

Genomic distribution of tRNAs in eukaryotes

The title says it all. I'm doing a literature search trying to see what is widely known and/or well established. I've found a couple of mentions that tRNAs are dispersed throughout the entire nuclear ...
6
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0answers
134 views

Comparative cost of RNA-seq vs sequencing full length cDNAs

I am in the process of assembling and annotating the genome of a non-model organism, using almost exclusively short read (paired-end Illumina) data. Throughput is one obvious benefit of these data ...
3
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0answers
56 views

RAD sequencing: choosing the appropriate enzyme?

I’m studying Darwin’s finches genome and I say in some articles that the researchers used restriction enzymes to cut the DNA in their double digest RAD protocol. They are using EcoRI and MseI (GAATTC ...
3
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0answers
58 views

Degree of dosage compensation in Drosophila melanogaster

In this paper the authors state that the dosage compensation seen in Drosophila is approximately twofold, but they do not provide any source or numbers (as far as I can see) for this. What is the mean ...
2
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0answers
16 views

Why there are two rounds of cytosine de-methylation in mammalian development?

I assume that the key biological meaning of cytosine de-methylation during germline development in germline progenitor cells is to reset imprinted genes and then set methylation pattern on these genes ...
2
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0answers
39 views

What is the best way to perform ultra-deep targeted sequencing of few samples?

I performed recent whole genome/exome sequencing in tumor samples and now I would like to take a few of these variants (say maximum 50 amplicons) to: 1) Validate them in the original samples 2) ...
2
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0answers
41 views

Where can I upload non-human Genotype data?

I have genotype data from few chicken population and I want to (need to) upload them somewhere online with free access. I have searched the web but I haven't found any place for non-human genotype ...
2
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0answers
43 views

Genome-wide methylation analysis: sources of technical error?

We are doing a genome-wide analysis of methylation via bisulfite sequencing for an insect species. Previous experimental techniques have suggested the presence of methylation in this organism, ...
2
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0answers
40 views

Assembly reconciliation

We have some bacterial genomes that were assembled using Spades, they were sequenced with and IonTorrent PGM. There are many assemblers and they give different results. I was interested in a tool ...
2
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0answers
106 views

Predicting host-pathogen gene interaction networks

Background What we have are: ~20 genome sequences for a host species that come with gene annotations Several sequenced genomes for parasite/pathogens of these hosts Question What are the ...
2
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0answers
184 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: ...
1
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0answers
30 views

Walkthrough Illumina Genotyping

I would love help outlining a basic walkthrough of the wet-lab techniques for processing blood samples from patients, all the way to loading a BeadChip, to the part just before Next Generation ...
1
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0answers
33 views

EMBOSS matcher and supermatcher - incongruent results?

I am trying to align a sequence to the mouse genome. I know a priori that part of my sequence should align to chromosome 9, but not all of it. I gathered that EMBOSS' ...
1
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0answers
68 views

“Gold standard” for CNV detection methods?

Is there a generally accepted "gold standard" for testing the performance of CNV detection methods? I'm interested both in learning about existing datasets that may serve as gold standards for CNV ...
1
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0answers
51 views

Paired-end mapping exercise

Pair-end mapping (PEM) is a technique that allows to detect structural variants in DNA by obtaining paired-end reads and the comparison of their positions in a reference genome. Then among libraries ...
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0answers
32 views

An elementary question for gene variation detection procedure in a paper

“Samples were divided into subtypes; each subtype was considered separately as a test set, using the remaining subtypes as the control. In our analysis, chromosome arms were subdivided into ...
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0answers
28 views

Walkthrough Analyzing/Processing Genotyping Data for Association Studies

I need help outlining the data analysis process of analyzing genotyping data you get back from a Next Generation Sequencing experiment. Here are the steps I currently believe you go through, but I ...
0
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0answers
69 views

How do I select the sequence identity threshold in cd-hit to cluster proteins for core genome comparative analysis?

Can anyone suggest a method for selecting the sequence identity threshold for protein clustering in cd-hit? If I use too high of a threshold, then the number of protein clusters shared between three ...
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0answers
24 views

Solid mouse (C57BL/6) WT primers

I am trying to get a good pair (or better yet, library of pairs) of primers that give me one band in WT mice (C57BL/6). Do you know where I could find such a thing? Alternatively, I thought of just ...