taxonomic classification with rna-seq data
Entering edit mode
3.3 years ago
vm.higareda ▴ 30

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.

taxonomy rnaseq Kraken kaiju IMSA+A • 933 views
Entering edit mode

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.


Login before adding your answer.

Traffic: 2872 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6