Can CIRI_DE_replicate be used for Differential expression analysis of DS_score

[tjhwangxiong]

Study without biological replicate, CIRI_DE generates DS_score.

In CIRI_DE_replicate output, only DE was generated. How can we get DS_score using CIRI_DE_replicate?

Thanks

[Kevinzjy]

No, CIRI_DE can not deal with multiple samples, you can use statistical tests like t-test or rank sum to measure junction ratio changes.

[tjhwangxiong]

No, CIRI_DE can not deal with multiple samples, you can use statistical tests like t-test or rank sum to measure junction ratio changes.

All my 10 samples (control: 5, case; 5) were sequenced using RNAse R pretreated RNA. I don't know whether the expression level of genes and transcripts is correct.

Moreover, CIRI_DE_replicate --lib library_info.csv \ --bsj circRNA_bsj.csv \ --gene gene_count_matrix.csv \ --out circRNA_de.tsv

Here is the sample list #sample.list WT1 ./WT1/WT1.gtf C 1 WT2 ./WT2/WT2.gtf C 2 WT3 ./WT3/WT3.gtf C 3 WT4 ./WT4/WT4.gtf C 4 WT5 ./WT5/WT5.gtf C 5 AD1 ./FAD1/FAD1.gtf T 1 AD2 ./FAD2/FAD2.gtf T 2 AD3 ./FAD3/FAD3.gtf T 3 AD4 ./FAD4/FAD4.gtf T 4 AD5 ./FAD5/FAD5.gtf T 5

I sorted the DE in circRNA_de.tsv, only 0, -1, 1 were found, is this normal?

Thanks.

[Kevinzjy]

The expression level of genes and transcripts could be quite different from normal poly(A) sequencing samples, and that's exactly the major limitation of circRNA analysis using RNase R treated libraries. But the circRNA differential expression results should be fine.

The final DE column indicates whether the corresponding gene is significantly change (-1 = down-upregulated / 1 = up-regulated / 0 = no significant change).