The study of genomes, the entire hereditary information of an organism.

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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 ...
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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 ...
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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, ...
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23 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 ...
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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 ...
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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: ...
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Referencing the homologous chromosomes

There exist a co-ordinate system from chromosomes like "12p11.3". In this system, first integer range from 1 to 23 i.e it takes homologous chromosomes as a pair. If we want to distinguish among ...
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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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“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 ...