text: user2757: I have used Deseq for estimating the differentially expressed introns for the RNA seq data using the UCSC intron bed file. can Deseq be used for differentially expressed intron analysis?
  
  user77: Typical tools to use for this would be the DEXseq packages (as done here) or rMATS, which will calculate intron retention rates.
  I would generally suggest not summing intronic counts by gene and using that in DESeq2 (I assume that's what you meant by DESeq, since there's no reason to use the original DESeq for anything). What you'd be getting if you did this is less expressed introns and more sample-specific bias in enriching for mature versus pre-mRNA.
  
original_text: 2757: <p>I have used Deseq for estimating the differentially expressed introns for the RNA seq data using the UCSC intron bed file. can Deseq be used for differentially expressed intron analysis?</p>
   77: <p>Typical tools to use for this would be the DEXseq packages (<a href="https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471142905.hg1116s87" rel="nofollow noreferrer">as done here</a>) or <a href="http://rnaseq-mats.sourceforge.net/" rel="nofollow noreferrer">rMATS</a>, which will calculate intron retention rates.</p>
  
  <p>I would generally suggest not summing intronic counts by gene and using that in DESeq2 (I assume that's what you meant by DESeq, since there's no reason to use the original DESeq for anything). What you'd be getting if you did this is less expressed introns and more sample-specific bias in enriching for mature versus pre-mRNA.</p>
  