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  • Bowtie-build - reference genome issue

    Hello!

    I`m new in NGS analysis, but in my new lab i had to replace my colleague in big NGS project related to miRNA-seq. He left me bunch of fastq`s and mirbase 21 fasta file with prebuilt indexes ("old" attached file). Recently, i`ve dowloaded mirbase 22 mature sequences as fasta, to try to map my reads to a newer version of database. I`ve changes U`s to T`s , and used bowtie-build to build new indexes)("new" attached file(renamed for upload). But when i run bowtie on the same samples with old file and the new one i had different results - ~35% unique mappers and ~4% multimappers with old mirbase 21 file i`ve got from colleague and exactly the opposite - 4% unique and ~35% multimappers - with the new file. As i said, i`m new in NGS analysis and i must be missing some simple processing step or something, that inverts my mapping results. Can you please explain what am i doing wrong and maybe give some links to good practical ngs course? Thank you!
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