Open zhuying412 opened 6 months ago
Why are the log2 values of the chrX in the female reference I constructed mostly around 1?
the command is： cnvkit.py reference -x female -f hg38.fa -t *.targetscoverage.cnn -a *.antitargetscoverage.cnn -o female.ref.cnn
cnvkit.py reference -x female -f hg38.fa -t *.targetscoverage.cnn -a *.antitargetscoverage.cnn -o female.ref.cnn
I already know that all the coverage files are from female samples. There are over 30 female samples.
the chr1 log2 vaues are around 0, but chrX og2 vaues are around 1. what‘s wrong?
chr1 2181928 2182263 PRKCZ,PRKCZ-AS1 0.0465799 273.164 0.570149 0.102951 chr1 2182264 2182492 PRKCZ,PRKCZ-AS1 0.193172 293.473 0.635965 0.101452 chr1 2182492 2182720 PRKCZ,PRKCZ-AS1 -0.041366 227.606 0.644737 0.0824622 chr1 2184580 2184700 PRKCZ,FAAP20 -0.0935414 198.135 0.575 0.137293 chr1 2184905 2185025 PRKCZ,FAAP20 0.0996912 227.46 0.541667 0.142527 chr1 2185277 2185513 PRKCZ,FAAP20 0.146021 257.41 0.563559 0.0843587 chr1 2186003 2186211 FAAP20 -0.673849 135.573 0.649038 0.222612 chr1 2189684 2189804 FAAP20,LOC112268219 -0.315712 168.489 0.633333 0.169231 chr1 2193638 2193910 FAAP20 -0.21091 165.574 0.709559 0.120812 chr1 2193997 2194133 FAAP20 0.116102 193.951 0.691176 0.119158 chr1 2198006 2198142 FAAP20 0.028836 227.538 0.514706 0.16853 chr1 2198753 2198988 FAAP20 -0.141123 196.836 0.625532 0.0923563 chr1 2201049 2201225 FAAP20 -0.216047 177.062 0.590909 0.166447 chr1 2203537 2203657 FAAP20 -0.0436205 189.697 0.641667 0.179415 chr1 2206120 2206240 FAAP20 -0.0783537 223.143 0.533333 0.115648 chr1 2206289 2206409 FAAP20 -0.079993 212.083 0.591667 0.149838
chrX 10500 44321 Antitarget 1.08409 0.594856 0.521155 0 0.38684 chrX 95321 133371 Antitarget -0.648439 0.180803 0.492799 0 0.610774 chrX 222846 283690 Antitarget 1.3595 0.739088 0.554069 0 0.26073 chrX 284190 284310 PLCXD1 1.01094 198.653 0.625 0.140288 chrX 288732 288869 PLCXD1 1.22612 248.165 0.613139 0.136515 chrX 290651 290771 PLCXD1 0.860269 176.082 0.608333 0.237648 chrX 291498 291654 PLCXD1 1.03318 216.189 0.602564 0.16052 chrX 293034 293218 PLCXD1 1.19191 237.609 0.646739 0.110555 chrX 299096 299335 PLCXD1 1.36617 280.226 0.640167 0.0932014 chrX 305075 305195 GTPBP6 1.27843 247.114 0.583333 0.121238 chrX 307359 307512 GTPBP6 1.30517 242.109 0.666667 0.116407 chrX 307731 307880 GTPBP6 1.16491 214.525 0.651007 0.102272 chrX 311418 311627 GTPBP6 1.50505 295.529 0.665072 0.119271 chrX 312765 312924 GTPBP6 1.16055 224.826 0.622642 0.159013 chrX 314123 314243 GTPBP6 1.3682 242.38 0.666667 0.141329
Why are the log2 values of the chrX in the female reference I constructed mostly around 1?
the command is：
cnvkit.py reference -x female -f hg38.fa -t *.targetscoverage.cnn -a *.antitargetscoverage.cnn -o female.ref.cnnI already know that all the coverage files are from female samples. There are over 30 female samples.
the chr1 log2 vaues are around 0, but chrX og2 vaues are around 1. what‘s wrong?