Hi, I am doing RNA-seq analysis, the pipeline is as follows: upload data > FastQC > Trimmomatic > HISAT2 > Feature counts > Deseq 2 > Annotate Deseq 2 output tables. The reference I used for annotation is “mm10. refgene.gtf.” However, the output shows just NA, like picture showed below, what is the problem?
Thanks for help！
Have you used just one sample (replicate) for DESeq 2? DESeq2 does not calculate p-values (signifiance) if you just use one replicate.
Thank you for your response, I have 4 replicates in each group. I just figure out the problem. When I did feature count, I used built-in mm10. When I annotate Deseq2 output, I used mm10 from other website. If I use the same mm10 when I did “feature count” and “annotate Deseq 2 output”. It works.
Thanks for your help