I have question related to the counts generated by software using FeatureCounts and Htseq. They both give very different results. For example
AluSx3 295781 MER5A 244353 MER41B 43925 MIR 1513933
AluSx3 88023 MER5A 111860 MER41B 18632 MIR 67211
What could be the reason for large difference and which tool we should take into account for our analysis. Currently I was trying to generate the counts for transposons.