Commit d9e0ab7d authored by Georgi Tushev's avatar Georgi Tushev
Browse files

test RUVSeq

parent eaf4d2a5
ERCC 2and3Hc2_R1.MACE.cleaned 2and3Hc3_R1.MACE.cleaned 4and5Hc2_R1.MACE.cleaned 4and5Hc3_R1.MACE.cleaned 6and7Hc2_R1.MACE.cleaned 6and7Hc3_R1.MACE.cleaned 80SHc2_R1.MACE.cleaned 80SHc3_R1.MACE.cleaned InputHc2_R1.MACE.cleaned InputHc3_R1.MACE.cleaned bigger7Hc2_R1.MACE.cleaned bigger7Hc3_R1.MACE.cleaned
ERCC 2and3Hc2 2and3Hc3 4and5Hc2 4and5Hc3 6and7Hc2 6and7Hc3 80SHc2 80SHc3 InputHc2 InputHc3 bigger7Hc2 bigger7Hc3
ERCC-00002 9140 12382 15199 9748 11895 9531 3575 6079 31329 26857 26377 9934
ERCC-00003 382 456 632 280 374 300 106 152 1438 1280 957 233
ERCC-00004 3920 4865 6757 3681 4579 3910 1274 1961 13739 11403 11893 3558
......
sample reads.raw reads.aligned reads.ercc reads.mito ratio.aligned ratio.ercc ratio.mito
2and3Hc2_R1.MACE.cleaned 6502897 5124752 58939 53339 78.807215 0.906350 0.820234
2and3Hc3_R1.MACE.cleaned 7693990 6060973 74730 50336 78.775421 0.971278 0.654225
4and5Hc2_R1.MACE.cleaned 9086127 7244897 101015 34267 79.735810 1.111750 0.377135
4and5Hc3_R1.MACE.cleaned 5901348 4706567 59028 14532 79.754100 1.000246 0.246249
6and7Hc2_R1.MACE.cleaned 4771834 3862606 72877 12133 80.945942 1.527233 0.254263
6and7Hc3_R1.MACE.cleaned 4655716 3758648 58274 8124 80.731900 1.251666 0.174495
80SHc2_R1.MACE.cleaned 1163641 822494 20707 41857 70.682796 1.779501 3.597072
80SHc3_R1.MACE.cleaned 1629758 1101244 33667 53700 67.571014 2.065767 3.294968
InputHc2_R1.MACE.cleaned 5831777 4305878 204928 101238 73.834751 3.513989 1.735972
InputHc3_R1.MACE.cleaned 4824334 3422604 173967 55973 70.944590 3.606031 1.160222
bigger7Hc2_R1.MACE.cleaned 10560307 8716563 194216 19836 82.540811 1.839113 0.187835
bigger7Hc3_R1.MACE.cleaned 3646327 2993304 60957 6142 82.090937 1.671737 0.168443
2and3Hc2 6502897 5124752 58939 53339 78.807215 0.906350 0.820234
2and3Hc3 7693990 6060973 74730 50336 78.775421 0.971278 0.654225
4and5Hc2 9086127 7244897 101015 34267 79.735810 1.111750 0.377135
4and5Hc3 5901348 4706567 59028 14532 79.754100 1.000246 0.246249
6and7Hc2 4771834 3862606 72877 12133 80.945942 1.527233 0.254263
6and7Hc3 4655716 3758648 58274 8124 80.731900 1.251666 0.174495
80SHc2 1163641 822494 20707 41857 70.682796 1.779501 3.597072
80SHc3 1629758 1101244 33667 53700 67.571014 2.065767 3.294968
InputHc2 5831777 4305878 204928 101238 73.834751 3.513989 1.735972
InputHc3 4824334 3422604 173967 55973 70.944590 3.606031 1.160222
bigger7Hc2 10560307 8716563 194216 19836 82.540811 1.839113 0.187835
bigger7Hc3 3646327 2993304 60957 6142 82.090937 1.671737 0.168443
#edgeR_RUVSeq
#
# RUVSeq
#
# georgi.tushev@brain.mpg.de
# Nov 2017
# load edgeR
library(edgeR);
library(RUVSeq);
# clean current variables
rm(list = ls());
# read counts
indata<-as.matrix(read.table("/Users/tushevg/Desktop/UTRPolyribosomes/countTable_UTRPolysomes_ERCC_21Nov2017.txt",stringsAsFactors=F, header=T, row.names=1));
......@@ -26,3 +26,5 @@ data.window = txt{4};
data.span = txt{5};
data.reads = txt{6};
data.counts = [txt{7:end}];
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