Dear all, Good evening. I finished sRNA annotation and quantification using short stack software (https://github.com/MikeAxtell/ShortStack). Then, I identified the differential expressed sRNA by DESeq2. Those DE-sRNAs were predicted its target mRNAs by psRNATarget platform (https://www.zhaolab.org/psRNATarget/). However, the DEsRNA- targeted mRNAs can not find the corresponding higher signals in mutant by using the bam file (mapping to reference genome) by bowtie aligner.
I am so confusing. If the sRNA is predicted to target a specific gene by psRNATarget platform, why there are no corresponding results of the reference genome alignment by using bowtie aligner?
I am looking forward to any suggestions and explanations.
Thank you so mcuh
Clarence
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I'm not sure if understand your question, but this is the situation, if you have a DEsRNA (up-regulated), you wouldn't expect mRNA expression of its target (or targets). If the sRNA is down-regulated (or depleted), you would expect the expression of its target (or targets). I worked with smallRNAs in the past, and most of the false positives I got, were caused by their low abundance. In addition to the DE value, I suggest taking a look at the number of reads mapping to the miRNA (in my case, I used a threshold of 100 reads). Besides, target predictors are not perfect (keep that in mind). I tried a bunch of miRNA target predictors ~4 years ago, and the best was from the DIANA tools (my specie was m. musculus). It includes evidence from experimentally validated targets.