Is there any good statistic way or tools to compare the read count difference between treatments?
The data is per-base sequencing read count, and we don’t know the exact distribution of the per-base read count (attached).
For example:
2 treatments (treatment1 & treatment2), 3 samples (biological repeat) in each treatment.
data table:
chrom position treatment1_1 treatment1_2 treatment1_3 treatment2_1 treatment2_2 treatment2_3
chr12 26229353 1 245 175 0 0 1
chr14 60833709 120 0 81 0 0 1
chr2 87516663 1 111 83 0 1 0
chr14 60802415 101 0 61 0 0 1
chr11 60356985 17 37 24 0 0 1
chr1 18300478 14 34 24 1 0 0
chr1 271501486 29 28 12 1 0 0
chr15 75932698 32 25 11 0 0 1
chr1 188326280 14 24 28 1 0 0
chr7 43038815 16 37 11 1 0 0
chr20 48971845 23 18 22 0 0 1
chr13 50030361 10 37 16 0 1 0
chr5 58346829 9 35 18 1 0 0
chr14 60803076 74 0 107 0 0 0
chr15 21554556 33 44 19 0 0 0
chr21 8881378 30 51 14 0 0 0
chrX 56348140 0 51 40 0 0 0
chr24 22387291 30 43 16 0 0 0
The aim is to know if there is significant difference between treatment1 and treatment2, a p value will be needed. Of course, if a FDR is also available, that will be fantastic.
Many thanks!
The data is per-base sequencing read count, and we don’t know the exact distribution of the per-base read count (attached).
For example:
2 treatments (treatment1 & treatment2), 3 samples (biological repeat) in each treatment.
data table:
chrom position treatment1_1 treatment1_2 treatment1_3 treatment2_1 treatment2_2 treatment2_3
chr12 26229353 1 245 175 0 0 1
chr14 60833709 120 0 81 0 0 1
chr2 87516663 1 111 83 0 1 0
chr14 60802415 101 0 61 0 0 1
chr11 60356985 17 37 24 0 0 1
chr1 18300478 14 34 24 1 0 0
chr1 271501486 29 28 12 1 0 0
chr15 75932698 32 25 11 0 0 1
chr1 188326280 14 24 28 1 0 0
chr7 43038815 16 37 11 1 0 0
chr20 48971845 23 18 22 0 0 1
chr13 50030361 10 37 16 0 1 0
chr5 58346829 9 35 18 1 0 0
chr14 60803076 74 0 107 0 0 0
chr15 21554556 33 44 19 0 0 0
chr21 8881378 30 51 14 0 0 0
chrX 56348140 0 51 40 0 0 0
chr24 22387291 30 43 16 0 0 0
The aim is to know if there is significant difference between treatment1 and treatment2, a p value will be needed. Of course, if a FDR is also available, that will be fantastic.
Many thanks!
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