I am working with metagenomes sequenced by Illumina. I have assembled my data prior with Velvet, but when I do assemblies using other assemblers, like SGA, I do not have same genes, but better quality (higher N50). I have inferred that some genes obtained using Velvet assembly exists in sample, but could not be recovered from SGA assembly. Is it normal? Could someone help me? I appreciate some references also.
Celio what you can do is take a check on its extraction and quantification. All these steps are essential for the library to be mounted so that the repeatability is good. Any questions my email is [email protected]. Hug and I am at your disposal.
Hey Nara. So, my library was already done. My data has been treated by two different ways:
First. We assembled using Velvet, and inferred the presence of a certain gene, which was amplified, sequenced and expressed.
Second. We reassembled crude data using String Graph Assembler, and annotated. After all, we could not find that gene.
My question is about the chances of this happen. I mean if different assemblers could yield different qualitative results.
Yes. They are different types of responses. Conversecom his / her advisor. For each data type, or each type of material, DNA, RNA, etc. we have to take into account the most appropriate model. Review step by step sequencing, type of barcode, the generation of clusters, etc. as the analyzes which review the question you really want answered. Pass me the step by step I will try to help you.
Dear Brazilian fellows,
This question is instigating to me because of a previous experience of mine. I got Illumina reads very fragmented. It was an attempt to assembly chromosomes but unsuccessful. So we thought, "Ok, let us try at least obtain the mitochondrial DNA!". In the process, depending on the software and it's chosen configuration parameters the assembly was always different! So I concluded: the only possibility to get something from such kind of data where exhaustively trying several configurations and statistically find about the presence or absence of the expected genes. I also had a similar experience about large chromosome assembly where some genes were pseudogenes in some version and normal genes in other versions. It makes me think about the possibility of several published genomes being wrong assembled, that another assembly can give us another DNA strand, slightly different from the previous one and only a statistically approach, assembling several versions and using several tools, can tell the real about those strands. Below is listed the article above mentioned.
Best regards,
Anderson Santos
Article Preliminary Characterization of Mitochondrial Genome of Meli...
You might find this article helpful in understanding the limitations of assembly.
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