Mapping >70%, very few counts in matrix

Question

[af1065]

Hi,

I have mapped reads to an assembled reference, and generated a count matrix.

Is there are way I can check for a reason my count matrix has 6/91000 counted transcripts, though the mapping percentage is high?

Thanks,

[jared.andrews07]

Check the 6 genes - what are they and why might they be accounting for so many of your reads? We can't help you beyond that without the code used for alignment and count generation.