taxonomic classification with rna-seq data
I have some single end RNA-seq data from Drosophila larvae and I would like to know what other microorganisms are present in my samples different to Drosophila.
Do you have any recommendation? I have read that kraken can do taxonomic classification with RNA-seq and also IMSA+A.
My RNA-seq libraries were not polyA enriched and I have a considerable number of reads that do not map to D. melanogaster genome.
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Kraken2 and Kaiju are a couple of programs you could use for microbial classification.
As for the reads that do not map you could take a sampleof non-mapping reads and do a quick blast search at NCBI. Hopefully any contamination is with one or two species and can be readily identified. If you have substantial contamination with non-expected species then the entire experiment may need to be reviewed for usability.