RNA-seq, how to detect contamination?
I would like to know if my data contains bacterial reads. And in that case delete it. Do you know any program to do it?
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AlonsoCid •
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FastQC does not detect reads from specific genomes. Are you referring to
Fastqscreen(which is a different program)? Do you know that your data will contain contamination (sometimes samples will have contaminants, they may be gut bacteria etc)? If not the "hits" you are seeing may simply be false positives.What is "exagen" reads?
I have change the post to make things more clear. Thanks for the answer.