Bioinformatic tools for removing bacterial contamination from Human SmallRNA sequencing data

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Problem with shRNA transfection. Why are only two plates getting contaminated instead of all?

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Rajesh Pal

You can use FASTQ-Screen for identification.

and for filtering, you can either go for BBDUK, SortmeRNA or SeqMonk

Rune Andreassen

Is it something you need to do? If you are e.g. doing expression analysis of miRNAs then you would use a reference miRNAom. These will count the miRNAs in your sample and any other reads would not interfere with this analysis.