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I am using Bowtie to remove non-coding RNAs (tRNA, snRNA, rRNA) by rfam and also maping our microRNA-seq data with mirbase using following code:

bowtie -m 10  -l 18 -n 1 -v 2 -e 80 --best --strata -a   genome.index.file    inputfastqfile   --un unaligned.fq

Unfortunately I dont have any references or index for that code. Are there any other settings and options to improve this code?

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  • $\begingroup$ Why rfam specifically? You can you rRNA, tRNA, and snRNA database to get their sequences (assuming human genome) and use a hierarchical sequence alignment strategy to remove all the ncRNAs and, finally, map the filtered sequences to miRNAs. $\endgroup$
    – Lot_to_learn
    Jun 30, 2021 at 5:51

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