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Commit 650b34e0 authored by Venkat Malladi's avatar Venkat Malladi
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Add in spike-in references.

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ERCC_spikein/spike_in_concentrations.tsv 0 → 100644
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Re-sort ID ERCC ID subgroup concentration in Mix 1 (attomoles/ul) concentration in Mix 2 (attomoles/ul) expected fold-change ratio log2(Mix 1/Mix 2)
1 ERCC-00130 A 30000 7500 4 2
2 ERCC-00004 A 7500 1875 4 2
3 ERCC-00136 A 1875 468.75 4 2
4 ERCC-00108 A 937.5 234.375 4 2
5 ERCC-00116 A 468.75 117.1875 4 2
6 ERCC-00092 A 234.375 58.59375 4 2
7 ERCC-00095 A 117.1875 29.296875 4 2
8 ERCC-00131 A 117.1875 29.296875 4 2
9 ERCC-00062 A 58.59375 14.6484375 4 2
10 ERCC-00019 A 29.296875 7.32421875 4 2
11 ERCC-00144 A 29.296875 7.32421875 4 2
12 ERCC-00170 A 14.6484375 3.66210938 4 2
13 ERCC-00154 A 7.32421875 1.83105469 4 2
14 ERCC-00085 A 7.32421875 1.83105469 4 2
15 ERCC-00028 A 3.66210938 0.91552734 4 2
16 ERCC-00033 A 1.83105469 0.45776367 4 2
17 ERCC-00134 A 1.83105469 0.45776367 4 2
18 ERCC-00147 A 0.91552734 0.22888184 4 2
19 ERCC-00097 A 0.45776367 0.11444092 4 2
20 ERCC-00156 A 0.45776367 0.11444092 4 2
21 ERCC-00123 A 0.22888184 0.05722046 4 2
22 ERCC-00017 A 0.11444092 0.02861023 4 2
23 ERCC-00083 A 0.02861023 0.00715256 4 2
24 ERCC-00096 B 15000 15000 1 0
25 ERCC-00171 B 3750 3750 1 0
26 ERCC-00009 B 937.5 937.5 1 0
27 ERCC-00042 B 468.75 468.75 1 0
28 ERCC-00060 B 234.375 234.375 1 0
29 ERCC-00035 B 117.1875 117.1875 1 0
30 ERCC-00025 B 58.59375 58.59375 1 0
31 ERCC-00051 B 58.59375 58.59375 1 0
32 ERCC-00053 B 29.296875 29.296875 1 0
33 ERCC-00148 B 14.6484375 14.6484375 1 0
34 ERCC-00126 B 14.6484375 14.6484375 1 0
35 ERCC-00034 B 7.32421875 7.32421875 1 0
36 ERCC-00150 B 3.66210938 3.66210938 1 0
37 ERCC-00067 B 3.66210938 3.66210938 1 0
38 ERCC-00031 B 1.83105469 1.83105469 1 0
39 ERCC-00109 B 0.91552734 0.91552734 1 0
40 ERCC-00073 B 0.91552734 0.91552734 1 0
41 ERCC-00158 B 0.45776367 0.45776367 1 0
42 ERCC-00104 B 0.22888184 0.22888184 1 0
43 ERCC-00142 B 0.22888184 0.22888184 1 0
44 ERCC-00138 B 0.11444092 0.11444092 1 0
45 ERCC-00117 B 0.05722046 0.05722046 1 0
46 ERCC-00075 B 0.01430512 0.01430512 1 0
47 ERCC-00074 C 15000 22500 0.67 -0.58
48 ERCC-00113 C 3750 5625 0.67 -0.58
49 ERCC-00145 C 937.5 1406.25 0.67 -0.58
50 ERCC-00111 C 468.75 703.125 0.67 -0.58
51 ERCC-00076 C 234.375 351.5625 0.67 -0.58
52 ERCC-00044 C 117.1875 175.78125 0.67 -0.58
53 ERCC-00162 C 58.59375 87.890625 0.67 -0.58
54 ERCC-00071 C 58.59375 87.890625 0.67 -0.58
55 ERCC-00084 C 29.296875 43.9453125 0.67 -0.58
56 ERCC-00099 C 14.6484375 21.9726563 0.67 -0.58
57 ERCC-00054 C 14.6484375 21.9726563 0.67 -0.58
58 ERCC-00157 C 7.32421875 10.9863281 0.67 -0.58
59 ERCC-00143 C 3.66210938 5.49316406 0.67 -0.58
60 ERCC-00039 C 3.66210938 5.49316406 0.67 -0.58
61 ERCC-00058 C 1.83105469 2.74658203 0.67 -0.58
62 ERCC-00120 C 0.91552734 1.37329102 0.67 -0.58
63 ERCC-00040 C 0.91552734 1.37329102 0.67 -0.58
64 ERCC-00164 C 0.45776367 0.68664551 0.67 -0.58
65 ERCC-00024 C 0.22888184 0.34332275 0.67 -0.58
66 ERCC-00016 C 0.22888184 0.34332275 0.67 -0.58
67 ERCC-00012 C 0.11444092 0.17166138 0.67 -0.58
68 ERCC-00098 C 0.05722046 0.08583069 0.67 -0.58
69 ERCC-00057 C 0.01430512 0.02145767 0.67 -0.58
70 ERCC-00002 D 15000 30000 0.5 -1
71 ERCC-00046 D 3750 7500 0.5 -1
72 ERCC-00003 D 937.5 1875 0.5 -1
73 ERCC-00043 D 468.75 937.5 0.5 -1
74 ERCC-00022 D 234.375 468.75 0.5 -1
75 ERCC-00112 D 117.1875 234.375 0.5 -1
76 ERCC-00165 D 58.59375 117.1875 0.5 -1
77 ERCC-00079 D 58.59375 117.1875 0.5 -1
78 ERCC-00078 D 29.296875 58.59375 0.5 -1
79 ERCC-00163 D 14.6484375 29.296875 0.5 -1
80 ERCC-00059 D 14.6484375 29.296875 0.5 -1
81 ERCC-00160 D 7.32421875 14.6484375 0.5 -1
82 ERCC-00014 D 3.66210938 7.32421875 0.5 -1
83 ERCC-00077 D 3.66210938 7.32421875 0.5 -1
84 ERCC-00069 D 1.83105469 3.66210938 0.5 -1
85 ERCC-00137 D 0.91552734 1.83105469 0.5 -1
86 ERCC-00013 D 0.91552734 1.83105469 0.5 -1
87 ERCC-00168 D 0.45776367 0.91552734 0.5 -1
88 ERCC-00041 D 0.22888184 0.45776367 0.5 -1
89 ERCC-00081 D 0.22888184 0.45776367 0.5 -1
90 ERCC-00086 D 0.11444092 0.22888184 0.5 -1
91 ERCC-00061 D 0.05722046 0.11444092 0.5 -1
92 ERCC-00048 D 0.01430512 0.02861023 0.5 -1
README.md
View file @ 650b34e0
......@@ -18,7 +18,7 @@ PARP-1 interacting snoRNA and DDX21
- fpkm.py: Take average FPKM of replicates
- diff_genes.sh: EBseq differential gene analysis
- rip_seq_rna_seq_analysis.py: Using STAR to analyze RIP-seq data
## Analysis of RIP-seq data
- RIP-seq.Rmd: Analysis of RIP-seq data
......@@ -32,3 +32,5 @@ PARP-1 interacting snoRNA and DDX21
- Summary_RIP-seq.xlsx: Summary of RIP-seq sequencing data bound RNA types
- Summary_RNA-seq.xlsx: Summary of RNA-seq for DDX21 perturbations
- Figures.pptx: Powerpoint of Figures
- reference_annotations: Reference annotations files
- ERCC_spikein: ERCC 92 spikein information
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