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eimd
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ipynbs
Notebook
gene_id gene_name sample1 sample2 fold_change direction total_fpkm q-value gene_description
CGI_10006532 . Troco Umbo 8.37 UP 55.29 0.00049485
CGI_10023338 . Troco Umbo 31.68 DOWN 152.66 0.00049485
EKC17242 CGI_10001446 Troco Umbo 3.76 DOWN 42.09 0.00049485
EKC17313 CGI_10001190 Troco Umbo 7.90 UP 16.74 0.00049485
EKC17492 CGI_10000706 Troco Umbo 14.59 DOWN 328.69 0.00049485
EKC17563 CGI_10000573 Troco Umbo 3.20 UP 3470.43 0.00049485
EKC17629 CGI_10000434 Troco Umbo 97.59 DOWN 416.64 0.00049485
EKC17663 CGI_10000384 Troco Umbo 3.91 UP 1535.08 0.00049485
EKC17667 CGI_10000377 Troco Umbo 182.69 DOWN 1851.02 0.00049485
In order to get enrichment you need to rely on SPID or other (here we use SPID as we have it). This means a simple join to get SPID that correspond to table above
processing chunk line 0 to 2988 (0.863645076752 s elapsed)
pushing /Volumes/web/cnidarian/fish546sort_gene.txt...
parsing 2D0D0BB8...
finished fish546_DEgene_out
!cat fish546_DEGjoinSPonly.txt
Now need to upload Backgroung list (all corresponding IDs in oyster genome)
!cat Cgigas_allSP.txt
--2014-02-08 10:26:32-- http://david.abcc.ncifcrf.gov/data/download/chart_B89D12125EAE1391883715950.txt
Resolving david.abcc.ncifcrf.gov... 129.43.1.164
Connecting to david.abcc.ncifcrf.gov|129.43.1.164|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 47347 (46K) [text/plain]
Saving to: `chart_B89D12125EAE1391883715950.txt'
100%[======================================>] 47,347 184K/s in 0.3s
2014-02-08 10:26:49 (184 KB/s) - `chart_B89D12125EAE1391883715950.txt' saved [47347/47347]
"id" "baseMean" "baseMeanA" "baseMeanB" "foldChange" "log2FoldChange" "pval" "padj"
"comp10002_c0_seq1" 5.11042261412799 6.56521445318632 3.65563077506966 0.556818181818182 -0.844721774522088 0.885218680234281 1
"comp10005_c0_seq1" 4.89904260332464 4.92391083988974 4.87417436675954 0.989898989898991 -0.0146467759644005 1 1
"comp10007_c0_seq1" 11525.6691667085 17587.3888682795 5463.94946513745 0.310674285197173 -1.68652526171154 0.147533184864772 1
"comp10008_c0_seq1" 6329.84902821593 6860.6491035797 5799.04895285216 0.845262432941859 -0.242528763050997 0.833689827988819 1
"comp10009_c0_seq1" 11933.5704169675 13182.9506219981 10684.1902119369 0.810455149100568 -0.303195746233489 0.792097629317823 1
"comp1000_c0_seq1" 24.3833059520802 42.6738939457111 6.09271795844943 0.142773892773893 -2.80819589849697 0.159574074144965 1
"comp10010_c0_seq1" 11.0290629166217 12.3097770997243 9.74834873351908 0.791919191919192 -0.336574870851763 0.936698849449615 1
"comp10012_c0_seq1" 2.25057540914152 3.28260722659316 1.21854359168989 0.371212121212121 -1.42968427524324 0.920190447196145 1
"comp10013_c0_seq1" 3.87944490415555 4.10325903324145 3.65563077506966 0.890909090909092 -0.16664986940945 1 1
comp42267_c0_seq1
comp27506_c0_seq1
comp31078_c0_seq1
comp42994_c1_seq12
comp43376_c0_seq11
comp43684_c0_seq63
comp43850_c0_seq2
comp23647_c0_seq1
comp37750_c2_seq5
comp14218_c0_seq1
comp38365_c0_seq23
comp42326_c1_seq2
comp42897_c0_seq4
comp41990_c0_seq3
comp39888_c0_seq2
comp41088_c0_seq3
comp22830_c0_seq1
comp33776_c1_seq2
comp9895_c0_seq2
comp34272_c0_seq1
comp43741_c0_seq9
comp19578_c0_seq1
comp28371_c1_seq1
comp44708_c0_seq2
comp38094_c0_seq2
comp46998_c0_seq1
comp7324_c0_seq1
comp30573_c0_seq1
comp42812_c1_seq2
comp40434_c1_seq2
comp38128_c0_seq1
comp37019_c0_seq1
comp29092_c0_seq2
comp43755_c0_seq29
comp36701_c0_seq7
comp39792_c1_seq4
comp44757_c0_seq12
comp41431_c0_seq1
comp42010_c0_seq2
comp38830_c0_seq3
comp41430_c0_seq1
comp19258_c0_seq1
comp34994_c0_seq1
comp37019_c0_seq9
comp35574_c1_seq2
comp7357_c0_seq1
comp33776_c1_seq3
comp9790_c0_seq2
comp30947_c0_seq1
comp10747_c0_seq1
comp28235_c0_seq1
comp30920_c0_seq1
comp30920_c1_seq1
comp33014_c0_seq7
comp34795_c4_seq2
comp44292_c0_seq1
comp43755_c0_seq14
comp40760_c0_seq3
comp39494_c0_seq7
comp40881_c2_seq3
comp43800_c0_seq2
comp43937_c0_seq7
comp44612_c0_seq13
comp40727_c0_seq1
comp35003_c0_seq2
comp38767_c1_seq4
comp28714_c1_seq1
comp33568_c0_seq2
comp36518_c0_seq7
comp43171_c0_seq2
comp41734_c0_seq1
comp38114_c0_seq2
comp44603_c0_seq5
comp42486_c0_seq1
comp35826_c3_seq1
comp35864_c0_seq3
comp36501_c1_seq2
comp9904_c0_seq1
comp44992_c0_seq1
comp33559_c0_seq2
comp39175_c0_seq4
comp42186_c0_seq7
comp25575_c0_seq1
comp36140_c0_seq1
comp7810_c0_seq1
comp40947_c0_seq2
comp44325_c2_seq1
comp37915_c0_seq2
comp38004_c0_seq1
comp16665_c0_seq1
comp30134_c0_seq1
comp34952_c0_seq1
comp37019_c0_seq14
comp18651_c1_seq1
comp39943_c0_seq3
comp39216_c0_seq1
comp26913_c0_seq4
comp44542_c1_seq2
comp42117_c0_seq2
comp38371_c0_seq1
comp39745_c1_seq10
comp42837_c1_seq2
comp37098_c0_seq5
comp23692_c0_seq2
comp40869_c0_seq2
comp11822_c0_seq1
comp40954_c0_seq1
comp30027_c0_seq1
comp36832_c0_seq1
comp46105_c0_seq1
comp41537_c0_seq5
comp38489_c0_seq2
comp38316_c0_seq1
comp39573_c0_seq3
comp37098_c0_seq7
comp37430_c6_seq1
comp44721_c0_seq5
comp30821_c0_seq3
comp36096_c1_seq2
comp41426_c1_seq3
comp43937_c0_seq5
comp44825_c0_seq2
comp38562_c2_seq4
comp29985_c0_seq1
comp44175_c0_seq9
comp28031_c0_seq1
comp42897_c0_seq7
comp24054_c1_seq1
comp39365_c0_seq10
comp40252_c2_seq4
comp42897_c0_seq5
comp37359_c0_seq1
comp20796_c1_seq1
comp22241_c0_seq1
comp22723_c0_seq1
comp31492_c0_seq3
comp36183_c1_seq1
comp36849_c3_seq1
comp10314_c0_seq1
comp23359_c0_seq2
comp38801_c1_seq7
comp46088_c0_seq1
comp38176_c0_seq1
comp39569_c0_seq1
comp42004_c0_seq1
comp27215_c0_seq1
comp26537_c0_seq3
comp43766_c3_seq1
comp36804_c4_seq9
comp34249_c2_seq1
comp46035_c0_seq1
comp44200_c0_seq12
comp31563_c0_seq2
comp46089_c0_seq1
comp27903_c0_seq1
comp42005_c0_seq5
comp20379_c0_seq1
comp41153_c1_seq2
comp41861_c0_seq8
comp44076_c0_seq18
comp41709_c1_seq5
comp40221_c0_seq2
comp30876_c0_seq1
comp37208_c0_seq5
comp42410_c0_seq3
comp37788_c0_seq2
comp7811_c0_seq1
comp44684_c0_seq2
comp19258_c3_seq1
comp39776_c0_seq4
comp32996_c0_seq11
comp31314_c0_seq1
comp36096_c1_seq1
comp41407_c0_seq1
comp40252_c1_seq1
comp41557_c0_seq5
comp38611_c0_seq21
comp41352_c1_seq2
comp31534_c1_seq1
comp42401_c0_seq2
comp34365_c0_seq2
comp35587_c0_seq1
comp33091_c2_seq2
comp35782_c0_seq2
comp25748_c0_seq1
comp38972_c0_seq2
comp10314_c0_seq2
comp15683_c0_seq1
comp41118_c0_seq2
comp43196_c0_seq3
comp43376_c1_seq1
comp44545_c1_seq1
comp47715_c0_seq1
comp37822_c0_seq1
comp39193_c0_seq2
comp36859_c0_seq1
comp41972_c4_seq8
comp7160_c0_seq1
comp41218_c1_seq13