So I've used salmon to extract readcount and use tximport to be used in DESeq2. After I perform DE analysis, there are some genes that has NA result. I suspects that this is caused by low count or maybe even 0 readcount result. Should I filter the low count gene before performing DE analysis using DESeq2 or I can just filter the NA result?
Before, I manually extract salmon result data and make it a matrix and then filter the low readcount. Then I import to DESeq2 using DESeq matrix loader function. With this tximport, I am a bit confused when should I filter the low count.