<p>In addition to swbarnes2 comment, I'd suggest a more systematic approach.</p>
<p><a href="https://ccb.jhu.edu/software/kraken2/index.shtml?t=manual" rel="nofollow noreferrer">Kraken2</a> is a tool for metagenomic analysis of reads, though it can be hard to set up.</p>
<p><a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1841-x" rel="nofollow noreferrer">mash screen</a> is another method for metagenomic analysis, much easier to set up but noisier.</p>
<p>If you are dealing with contamination, treating your data as metagenomic might help.</p>
<p>Also, as always, ensure that your workflow and reference assembly are correct!!!</p>

CC BY-SA 4.0
2022-04-01T23:05:45.727Z
2022-04-01T23:05:45.727Z
Maximilian Press
<p>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) <a href="https://i.sstatic.net/SlasJ.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/SlasJ.png" alt="fwd" /></a>. <a href="https://i.sstatic.net/IjGT8.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/IjGT8.png" alt="reverse" /></a> After mapping with the reference genome using bbsplit but the mapping is only 0.62%.</p>
<p>Any help/suggestions highly appreciated.</p>
<p>Thanks</p>

CC BY-SA 4.0
2022-03-16T01:34:22.403Z
Well, when you looked at the sequences of some of your reads, what species did they BLAST to?
swbarnes2
<rna-seq><read-mapping>
Low mapping reads for RNA sequence
# Low mapping reads for RNA sequence

(Asked by: username_0 on 2022-03-14)

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](https://i.sstatic.net/SlasJ.png)](https://i.sstatic.net/SlasJ.png). [![reverse](https://i.sstatic.net/IjGT8.png)](https://i.sstatic.net/IjGT8.png) After mapping with the reference genome using bbsplit but the mapping is only 0.62%.

Any help/suggestions highly appreciated.

Thanks

**Tags:** rna-seq, read-mapping
> **Comments:**
> **username_1**: Well, when you looked at the sequences of some of your reads, what species did they BLAST to?  

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## 1 answers

### Answer by username_2 on 2022-04-01. Score: 1

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

[Kraken2](https://ccb.jhu.edu/software/kraken2/index.shtml?t=manual) is a tool for metagenomic analysis of reads, though it can be hard to set up.

[mash screen](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1841-x) 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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