Why most genes have high padj values
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26 days ago
mnx0723 • 0

After receiving the pair-end fastq file, we obtained the expression matrix through Trimmomatic, STAR, and faetureCounts. I ran the program using all the basic options. After that, we will try to find different expression genes using DESeq2. The following is my data. When filtered based on padj<0.05, the number was much smaller than other samples. After checking the table, the p-value itself was basically high, but there were many padj values higher than 0.05 and many NA values.

I'm not sure what exactly went wrong, but if this problem occurred in pair-end compared to single-end, can you tell me which protocol was the problem?

![enter image description here][1]

dim(deseq_result_200805_1)
  [1] 33850     6
filtered_200805_1 <- deseq_result_200805_1 %>% filter(deseq_result_200805_1$padj<0.05)
dim(filtered_200805_1)
  [1] 788   6
RNA-seq DEG • 336 views
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Sorry, I made edits.

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788 differential genes is a lot. What is the problem?

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In the case of other samples, the total number of genes is at least 3,000 more than that one, but it seems to be a relatively small number. I guess I was in a bit of a hurry

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You want ~3000 DE genes?

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