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Could you provide some more details,like the command you gave etc..
In addition to what Jeffin Rockey said, since you tagged this as "rna-seq", you should be warned that bowtie2 is not appropriate for RNAseq data. Use STAR or something similar instead.
Unless it's prokaryotic RNA-seq?
Yes its RNA seq from cow ...
Please use
ADD REPLYto answer to earlier comments, as such this thread remains logically structured and easy to follow.For RNA-seq alignment of eukaryotic genomes you need a spliced aligner, most recommended nowadays are STAR and HISAT2.