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I am new to RNA sequencing analysis. I have RNA samples for bacteria for different treatment. I did contaminant filtration, remove adapters and checked fastQC report: attached below for one sample (fwd and rev) fwd. reverse After mapping with the reference genome using bbsplit but the mapping is only 0.62%.

Any help/suggestions highly appreciated.

Thanks

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    $\begingroup$ Well, when you looked at the sequences of some of your reads, what species did they BLAST to? $\endgroup$
    – swbarnes2
    Mar 16, 2022 at 1:34

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In addition to swbarnes2 comment, I'd suggest a more systematic approach.

Kraken2 is a tool for metagenomic analysis of reads, though it can be hard to set up.

mash screen is another method for metagenomic analysis, much easier to set up but noisier.

If you are dealing with contamination, treating your data as metagenomic might help.

Also, as always, ensure that your workflow and reference assembly are correct!!!

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