On the one hand, I have a bacterial draft genome, on the other hand I have contigs assembled from transcriptomic reads. I also have the predicted protein-coding sequences of the transcriptomics data.
I want to look into the transcriptomic contigs for some genes that I have already found in the genome. Is it possible? I would like to have the whole genome linked with those data
Abhijeet Singh
Generally Blast2Go is used for the transcriptomics data for the annotation, but as you say you already have the coding sequence, you can blast it against the whole genome.
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Vikash K. Singh
Do NCBI blastn by taking your transcriptomic contigs as query and CDS of bacterial genome as database and take best hit.
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