To get a file of only uniquely mapped reads (RNA star)

I ran my RNAseq data using RNA STAR and I want to get only the uniquely mapped reads for further analysis. how can I get that. I tried to use filtering tools where I could filter bam files but I couldn’t understand how to use them (I also checked some previous questions).

Hi @Ouns87

Try Filter BAM with this setting MapQ = 30.

Other options could include: Primary Alignment and Proper Pairs (if your data is paired).

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