Different alignment results on mirnaseq data upon using Bowtie vs Bowtie2.

Question

[Barninee]

Hi, I aligned my mirna seq data against hsa.gff3 file using bowtie first. However, upon generating the read count file (using bedtools) and running deseq2 on it, very few mirnas were observed. Also the PCA plot showed too much variance between control data. However, upon running the same on Bowtie2, I got a lot more differentially expressed mirnas. Is this normal? If so why is there such a stark difference?

[ATpoint]

Yes, no, maybe. You really need to add code and plots for these sorts of quesstions to be remotely comprehensible and reproducible.

[biofalconch]

Without the actual commands it is very difficult to pinpoint what the problem is.