To get a file of unmapped reads after RNA star

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Hello,
I am looking to get a file of unmapped reads after RNA star. How do I get that

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Hi @NIKITA_JHAVERI You are after any BAM filtering tool. Alternatively, consider HiSAT2 instead of RNA_STAR and in advanced options > outputs activate Write unaligned reads (in fastq format) to separate file(s).
Hope this helps.
Kind regards,
Igor

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