Deferentially expressed circRNAs with biological replicate

[ravisaroch]

Hello, I used CIRIquant to calculate the fold change under a certain situation.

I used the sample as text files:

Ciriquant output file: 24_PAU_Case_1 ./AK10_S10.gtf T 1 24_PAU_Case_2 ./AK11_S11.gtf T 2 24_PAU_Case_3 ./AK12_S12.gtf T 3 0_PAU_Control_1 ./AK4_S4.gtf C 1 0_PAU_Control_2 ./AK5_S5.gtf C 2 0_PAU_Control_3 ./AK6_S6.gtf C 3

The below command is use to calculate DE circRNAs CIRI_DE_replicate --lib 0_24h_PAU_lib.csv --bsj 0_24h_PAU_circRNA_bsj.csv --gene 0_24_PAU_gene_count_matrix.csv --out 0_24_PAU_DE_Cir.tsv

It Generate Output file of the DE CircRNA

Circ_ID logFC logCPM LR PValue DE FDR 4:31022314|31029529 -7.64922634263453 -0.161626549205444 15.0799339995342 0.000103052931416515 0 0.0867705682527054 12:11277575|11320618 6.69328375381015 -1.50848617923073 13.7678102531273 0.000206850296297323 0 0.0870839747411729 12:11262912|11265838 7.65742002735099 -1.98591121764622 12.4043376775065 0.00042833770549839 0 0.120220116009881 3:19812063|19865665 -5.97369371848626 -1.97194836747005 9.66092614644816 0.00188228702661538 0 0.396221419102538 6:3094946|3106151 -6.41385190127333 -3.14131472782527 9.1566548978384 0.00247815160571721 0 0.417320730402778 10:18675348|18689873 7.72459306313907 -1.49011568946911 8.45368794039285 0.00364303965091808 0 0.42321854074561 5:7746966|7747829 5.77609936483112 -3.49785553816328 7.09539540202189 0.00772822404188243 0 0.42321854074561 5:19412253|19472056 -6.72256499136888 -2.65499597431979 7.0899583310074 0.00775170495334329 0 0.42321854074561 9:13492161|13598089 -6.30654725571083 -2.98243003713085 6.46588024949127 0.0109965158338529 0 0.42321854074561

Question: I'm curious whether the positive logFC value indicates an up-regulated circRNA in the case or control condition.

For example 6.69328375381015 is up regulated circRNA is case or in control condition?

[Kevinzjy]

Hi, @ravisaroch. The positive logFC means the circRNA is upregulated in the T group compared to the C group.