RNA transfer between human circulating cells and bacteria or contamination?

Question

[bart]

Hi,

I'm new to RNA seq and I am analyzing FASTQ files from RNA inside human circulating cells. Using Kraken2, I'm seeing that there are some reads from bacteria (see Krona pie chart). My question is: would it be possible to that these originate from bacteria present inside the body due RNA transfer from bacteria to the circulating cells? Or are they present due to contamination during the lab experiment? Is it possible to differentiate between these two options (contamination vs transfer?)

Answer 1

[Istvan Albert]

I would recommend investigating the results more closely and look for things like the accuracy of the classification, how many different bacteria/transcripts seem to be present

As a next step, if you were to extract and map the reads that were classified as that organism how well do those reads cover the expected "contaminants".

Can you recover reasonably full transcripts? or all reads are covering the same tiny fragment of the genome. How well do the reads match?

Most often what you will find are reads that only match partially, and only in a single tiny, region, and that would indicate artifacts of the sequencing process.