I have a question about gsMapper I'm hoping someone can help me with.
I have a project in which 20 samples underwent RNAseq using 454. I combined the SFFs and used gsAssembler to create a transcriptome.
Now, I want to use this transcriptome as a reference for individually mapping each of the 20 samples. From there I will ascertain differential expression data, etc. The transcriptome assembly resulted in 454AllContigs files and 454Isotigs files. Which should I use for the mapping reference??
I think it should be the 454AllContigs file, since mapping to the isotigs will results in a single read likely mapping to many different isotigs that share exons within an isogroup. I've read a different post that talked about finding the isotigs that contains the most exons in the isogroup, and only mapping to such a collection of long isotigs, but this seems like it would be less biologically relevant and simply more convenient.
Any thoughts are much appreciated
I have a project in which 20 samples underwent RNAseq using 454. I combined the SFFs and used gsAssembler to create a transcriptome.
Now, I want to use this transcriptome as a reference for individually mapping each of the 20 samples. From there I will ascertain differential expression data, etc. The transcriptome assembly resulted in 454AllContigs files and 454Isotigs files. Which should I use for the mapping reference??
I think it should be the 454AllContigs file, since mapping to the isotigs will results in a single read likely mapping to many different isotigs that share exons within an isogroup. I've read a different post that talked about finding the isotigs that contains the most exons in the isogroup, and only mapping to such a collection of long isotigs, but this seems like it would be less biologically relevant and simply more convenient.
Any thoughts are much appreciated
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