Commit 88ceeec0 authored by Venkat Malladi's avatar Venkat Malladi

Restructuring of RIP-seq analysis.

parent f3cacb0d
PARP-1 interacting snoRNA and DDX21
=================================
## External Repositories used in analysis:
## External Data used in analysis:
##Requirements:
- bedtools v2.25.0
- UCSC tools
- bedops v2.2.14
## Analysis of RIP-seq data
- RIP-seq.Rmd: Analysis of RIP-seq data
- figures: Figures related to RIP-seq binding
- tables: Tables of RIP-seq binding
## Analysis of RNA-seq
## General Analysis
- 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
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......@@ -63,7 +63,7 @@ chr5 138611868 138612009 + ENST00000516404.1 ENSG00000252213.1 0 227.62094058611
chr5 138614469 138614667 + ENST00000364089.1 ENSG00000200959.1 11.3876814530244 486.28110034307 SNORA74A-201 SNORA74A
chr5 172447730 172447931 + ENST00000391100.1 ENSG00000212402.1 179.483456931251 824.125889844779 SNORA74B-201 SNORA74B
chr5 40790178 40790306 - ENST00000391265.1 ENSG00000212567.1 0 48.530069489883 SNORA57.2-201 SNORA57
chr5 40832757 40832837 - ENST00000390994.1 ENSG00000212296.1 28.1845115962355 271.768389143345 SNORD72-201 SNORD72
chr5 40832757 40832837 - ENST00000390994.1 ENSG00000212296.1 28.1845115962354 271.768389143345 SNORD72-201 SNORD72
chr5 76376258 76376396 - ENST00000458862.1 ENSG00000238961.1 32.677694604331 97.5290285400547 SNORA47-201 SNORA47
chr5 82360022 82360156 - ENST00000459004.1 ENSG00000238835.1 67.306296349219 231.785406518844 SCARNA18-201 SCARNA18
chr5 137896731 137896799 - ENST00000384262.1 ENSG00000206989.1 0 30.4502396799266 SNORD63-201 SNORD63
......@@ -84,7 +84,7 @@ chr7 56128162 56128295 + ENST00000384439.1 ENSG00000207168.1 0 23.3528153936279
chr7 65220512 65220646 + ENST00000383907.1 ENSG00000206634.1 0 247.237766953434 SNORA22-201 SNORA22
chr7 107243807 107243952 + ENST00000459477.1 ENSG00000238832.1 0 21.4201686024311 snoU109.4-201 snoU109
chr7 129959118 129959222 + ENST00000459210.1 ENSG00000238336.1 0 19.9097720984135 snoU13.25-201 snoU13
chr7 45024976 45025109 - ENST00000384215.1 ENSG00000232956.4 67.8123587277846 194.606794946899 SNHG15-201 SNHG15
chr7 45024976 45025109 - ENST00000384215.1 ENSG00000232956.4 67.8123587277845 194.606794946899 SNHG15-201 SNHG15
chr7 45143947 45144081 - ENST00000384111.1 ENSG00000206838.1 0 200.880685649665 SNORA5A-201 SNORA5A
chr7 45144504 45144641 - ENST00000364902.1 ENSG00000201772.1 0 22.6709813675366 SNORA5C-201 SNORA5C
chr8 99054313 99054445 - ENST00000384339.1 ENSG00000207067.1 0 31.3729742156819 SNORA72-201 SNORA72
......@@ -103,7 +103,7 @@ chr10 120820494 120820623 - ENST00000410656.1 ENSG00000222588.1 0 8.025644566802
chr11 3943796 3943933 + ENST00000384249.1 ENSG00000206976.1 0 15.1139875783577 SNORA7.4-201 SNORA7
chr11 8705773 8705903 + ENST00000364113.1 ENSG00000200983.1 17.3443148284526 119.458632590481 SNORA3-201 SNORA3
chr11 8706985 8707116 + ENST00000391305.1 ENSG00000212607.1 34.4238309572341 252.899700547787 SNORA45-201 SNORA45
chr11 9450319 9450501 + ENST00000365128.1 ENSG00000201998.1 495.551852241503 1308.35645218146 SNORA23-201 SNORA23
chr11 9450319 9450501 + ENST00000365128.1 ENSG00000201998.1 495.551852241502 1308.35645218146 SNORA23-201 SNORA23
chr11 62432893 62433042 + ENST00000383870.1 ENSG00000206597.1 0 118.122406275151 SNORA57-201 SNORA57
chr11 75115464 75115610 + ENST00000384714.1 ENSG00000207445.1 0 49.6380619439899 SNORD15B-201 SNORD15B
chr11 93454707 93454787 + ENST00000364329.1 ENSG00000254911.2 0 103.53081491175 SCARNA9-202 SCARNA9
......@@ -253,7 +253,7 @@ chr5 178311715 178311880 + ENST00000383897.1 ENSG00000206624.1 0 31.372974215681
chr5 125888993 125889094 - ENST00000363477.1 ENSG00000200347.1 0 10.2505757338367 RNU6-963P-201 RNU6-963P
chr6 76353799 76353893 + ENST00000516689.1 ENSG00000252498.1 0 11.0139164799734 RNU6-1016P-201 RNU6-1016P
chr7 138561104 138561211 - ENST00000362776.1 ENSG00000199646.1 0 9.67577709455611 RNU6-1272P-201 RNU6-1272P
chr8 42928616 42928761 + ENST00000363861.1 ENSG00000200731.1 15.5500753634403 35.7002810040518 RNU1-124P-201 RNU1-124P
chr8 42928616 42928761 + ENST00000363861.1 ENSG00000200731.1 15.5500753634402 35.7002810040518 RNU1-124P-201 RNU1-124P
chr8 99204432 99204541 - ENST00000516749.1 ENSG00000252558.1 0 18.9964798003212 RNU6-914P-201 RNU6-914P
chr9 33868537 33868663 + ENST00000515939.1 ENSG00000251748.1 0 8.21673134220241 RNU4ATAC11P-201 RNU4ATAC11P
chr9 134002376 134002478 + ENST00000516813.1 ENSG00000252622.1 0 20.3001597866177 RNU6-881P-201 RNU6-881P
......
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