taxonomic classification with rna-seq data
0
0
Entering edit mode
22 months ago
vm.higareda ▴ 20

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 • 644 views
ADD COMMENT
1
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.

ADD REPLY

Login before adding your answer.

Traffic: 2748 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

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

Powered by the version 2.3.6