Hello, I have been using your software for a while now with ATAC-seq data and it has always worked really well. But I recently got a batch of samples that show always 0.4992 FREEMIX value and variable CHIPMIX value. I am not sure why this might be happening and I was wondering if you could give me some hint on what might be causing this behaviour. This is how some of my results look like (I have changed the SEQ_IDs to preserve anonymity)
#SEQ_ID RG CHIP_ID #SNPS #READS AVG_DP FREEMIX FREELK1 FREELK0 FREE_RH FREE_RA CHIPMIX CHIPLK1 CHIPLK0 CHIP_RH CHIP_RA DPREF RDPHET RDPALT
A1 ALL A1 96975 197168 2.03 0.49992 90727.84 95950.33 NA NA 0.47341 83263.18 131002.00 NA NA 2.032 1.0069 0.9824
A2 ALL A2 96975 125869 1.30 0.49992 58829.31 61262.93 NA NA 0.41467 51691.65 78533.83 NA NA 1.299 1.0003 0.9969
A3 ALL A3 96975 60686 0.63 0.49992 28853.20 29712.30 NA NA 0.53910 26535.65 45740.29 NA NA 0.627 0.9882 1.0325
A4 ALL A4 96975 79771 0.82 0.15866 35756.20 36028.39 NA NA 0.16279 25616.25 30493.15 NA NA 0.826 0.9979 0.9596
A5 ALL A5 96975 49830 0.51 0.49992 23741.71 24320.85 NA NA 0.70174 23126.33 45112.29 NA NA 0.514 0.9944 1.0162
A6 ALL A6 96975 286695 2.96 0.29665 125206.03 131321.59 NA NA 0.24873 102783.23 135801.39 NA NA 2.962 0.9890 1.0211
A7 ALL A7 96975 235164 2.42 0.45008 105989.76 111198.07 NA NA 0.29529 88608.68 123301.40 NA NA 2.421 1.0005 1.0191
A8 ALL A8 96975 106980 1.10 0.49992 50029.83 51962.34 NA NA 0.41218 43782.92 67128.11 NA NA 1.109 0.9891 0.9794
A9 ALL A9 96975 181847 1.88 0.00200 71410.23 71410.78 NA NA 0.00355 42320.27 42359.72 NA NA 1.881 0.9965 0.9706
Could it be related to high levels of duplication? Thank you in advance.
Hello, I have been using your software for a while now with ATAC-seq data and it has always worked really well. But I recently got a batch of samples that show always 0.4992 FREEMIX value and variable CHIPMIX value. I am not sure why this might be happening and I was wondering if you could give me some hint on what might be causing this behaviour. This is how some of my results look like (I have changed the SEQ_IDs to preserve anonymity)
#SEQ_ID RG CHIP_ID #SNPS #READS AVG_DP FREEMIX FREELK1 FREELK0 FREE_RH FREE_RA CHIPMIX CHIPLK1 CHIPLK0 CHIP_RH CHIP_RA DPREF RDPHET RDPALT
A1 ALL A1 96975 197168 2.03 0.49992 90727.84 95950.33 NA NA 0.47341 83263.18 131002.00 NA NA 2.032 1.0069 0.9824
A2 ALL A2 96975 125869 1.30 0.49992 58829.31 61262.93 NA NA 0.41467 51691.65 78533.83 NA NA 1.299 1.0003 0.9969
A3 ALL A3 96975 60686 0.63 0.49992 28853.20 29712.30 NA NA 0.53910 26535.65 45740.29 NA NA 0.627 0.9882 1.0325
A4 ALL A4 96975 79771 0.82 0.15866 35756.20 36028.39 NA NA 0.16279 25616.25 30493.15 NA NA 0.826 0.9979 0.9596
A5 ALL A5 96975 49830 0.51 0.49992 23741.71 24320.85 NA NA 0.70174 23126.33 45112.29 NA NA 0.514 0.9944 1.0162
A6 ALL A6 96975 286695 2.96 0.29665 125206.03 131321.59 NA NA 0.24873 102783.23 135801.39 NA NA 2.962 0.9890 1.0211
A7 ALL A7 96975 235164 2.42 0.45008 105989.76 111198.07 NA NA 0.29529 88608.68 123301.40 NA NA 2.421 1.0005 1.0191
A8 ALL A8 96975 106980 1.10 0.49992 50029.83 51962.34 NA NA 0.41218 43782.92 67128.11 NA NA 1.109 0.9891 0.9794
A9 ALL A9 96975 181847 1.88 0.00200 71410.23 71410.78 NA NA 0.00355 42320.27 42359.72 NA NA 1.881 0.9965 0.9706
Could it be related to high levels of duplication? Thank you in advance.