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Identify and remove contaminations in RNA-Seq dataset

Hi,

I am working with RNA-Seq Illumina PE – 150 bp dataset. I was wondering if there is a way to identify contaminations (such as mitochondrial DNA contamination, any other types of contamination) in the data, and remove the same?

Can this be removed pre or post alignment or maybe filter by reads?

Best Regards,

Abdul

rsem fastqc quantification alignment fastp
• 2,627 views • link
written by Abdul • Abdul

They would be removed post alignment, because you can't tell what a sequence represents until you align it to something. However, without knowing your specific purpose, or what you're trying to achieve, it's hard to recommend a specific strategy. You can filter your BAM files to remove certain alignment targets (e.g. Mitochondrial DNA), or you can generate counts on features and remove the features you want to ignore (i.e. rows in your count table representing mitochondrial genes, etc.). All come with caveats for your analysis.

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written by seidel seidel

seidel Thank you for the feedback. I am working on the gene counts file filtered to include the only protein coding genes and lncRNAs.

I was quickly going through the script and assume that FASTQ files were assessed using FastQC > aligned using bowtie2 with inclusion of chrM in the reference > filtered + trimmed using fastp > quantified using rsem to obtain gene counts > filtered to include protein coding genes and lncRNAs.

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written by Abdul • Abdul

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