1 Overview of tsRNAsearch analysis comparing CytC versus TotalRNA

1.1 Quantities of ncRNA features identified

1.1.1 Number of raw reads identified for each ncRNA group

1.1.2 Proportions of ncRNA groups identified (normalised by reads per million)

1.1.3 Proportions of ncRNA groups identified (all samples, normalised by reads per million)

1.2 Venn diagram comparing the three methods used (DESeq2, distribution algorithm, cleavage algorithm)

1.2.1 Details of the intersections can be found here:

  • ...Data/VennDiagramGeneration/CytC_vs_TotalRNA.intersect…

1.2.2 Files used to generate the Venn Diagram can be found here:

  • ...Data/VennDiagramGeneration

1.3 Summary Report Table

Top 20 results shown (sorted by distribution score)
feature slope.score Fishers.method.pvalue distribution.score DESeq2.Log2FC DESeq2.pvalue DESeq2.padj cleavage.score
GlyGCC 314155.049 0.0000000 11277.364 NA NA NA NA
Val 303941.118 0.0000000 19074.385 NA NA NA 23687319.1
GlyCCC 152887.596 0.0000000 7592.334 NA NA NA NA
ENSMUSG00000092998 (Mir5099) 125730.003 0.0000000 36319.736 3.7560814 0.0000000 0.0000000 37234475.7
ValCAC 75219.156 0.0000002 4057.715 0.7499996 0.0630639 0.1322865 5101647.2
LysCTT 63856.215 0.2097641 3049.099 -0.0218859 0.9529760 0.9529760 46526580.9
GluCTC 47755.916 0.0000000 20639.234 0.0391343 0.9255359 0.9529760 13962563.2
ArgTCT 41106.248 0.0000000 113526.736 0.7225153 0.2330568 0.3088003 108859109.7
CysGCA 33049.813 0.0000000 27178.009 -3.8541300 0.0000008 0.0000084 4334959.1
LysTTT 27509.196 0.0000000 172910.160 4.4876410 0.0000000 0.0000001 10564825.0
ENSMUSG00000065922 (n-R5-8s1) 26371.763 0.1384756 43692.462 2.9885247 0.0000066 0.0000498 3576746.3
ArgCCT 22715.322 0.0000000 8334.162 -3.5036150 0.0001003 0.0005908 453341.1
ENSMUSG00000084667 (Gm23212) 16539.744 0.0000000 374364.238 6.8606585 0.0000023 0.0000205 1564417.7
HisGTG 13869.156 0.7752664 2547.189 NA NA NA NA
ENSMUSG00000064500 (Gm25296) 10361.264 0.0000000 120443.892 6.0657928 0.0001817 0.0009629 2563440.5
MetCAT 9392.816 0.0000000 2973.051 1.3402278 0.0976291 0.1784256 592825.1
ENSMUSG00000077797 (Snord19) 9111.062 0.0000000 140955.930 6.4161988 0.0000435 0.0002882 230098.7
AspGTC 6147.152 0.0000000 5508.929 -0.3292130 0.7588220 0.8378660 603522.5
ENSMUSG00000065378 (Gm22744) 6083.708 0.0000000 66405.980 5.2134472 0.0062729 0.0251689 328807.0
ENSMUSG00000064780 (Snord95) 5343.119 0.0000000 105037.467 4.9119721 0.0154228 0.0480828 959292.0

1.4 tRNA Read Alignment Length

2 Differential Expression Results (DESeq2)

2.1 Overview of DE analysis

2.1.1 Principal Component Analysis (PCA) of all samples

2.1.2 Sample distance matrix

2.1.3 Volcano plot showing differentially expressed genes

2.2 Features identified

2.2.1 Differentially expressed tRNAs

2.2.2 Coverage plots for all differentially expressed tRNAs

2.2.3 Differentially expressed ncRNAs (other than tRNAs)

2.2.4 Coverage plots for all differentially expressed ncRNAs

Full results for features differentially regulated in CytC versus TotalRNA here:

  • ...Data/DE_Results/DESeq2/CytC_vs_TotalRNA_DESeq2-output.csv
  • ...Data/DE_Results/DESeq2/CytC_vs_TotalRNA_DESeq2-output-upregulated.csv
  • ...Data/DE_Results/DESeq2/CytC_vs_TotalRNA_DESeq2-output-downregulated.csv

3 Distribution Algorithm Results

3.1 Feature identified

3.1.1 Highest scoring tRNA fragments identified using the distribution algorithm

Full results here:

  • ...Data/Distribution_results/CytC_vs_TotalRNA_High-distribution-tsRNAs.txt

3.1.2 Coverage plots for all tRNAs with irregular distribution identified by the distribution algorithm

3.1.3 Highest scoring ncRNA fragments identified using the distribution algorithm

Full results here:

  • ...Data/Distribution_results/CytC_vs_TotalRNA_High-distribution-ncRNAs.txt

3.1.4 Coverage plots for all ncRNAs with irregular distribution identified by the distribution algorithm

4 Slope Algorithm Results

4.1 Features identified

4.1.1 Highest scoring tRNA fragments identified using the slope algorithm

Full results here:

  • ...Data/Slope_results/CytC_vs_TotalRNA_High-slope-tRNAs.txt

4.1.2 Coverage plots for all tRNAs with significantly different slopes identified by the slope algorithm

4.1.3 Highest scoring ncRNA fragments identified using the slope algorithm

Full results here:

  • ...Data/Slope_results/CytC_vs_TotalRNA_High-slope-ncRNAs.txt

4.1.4 Coverage plots for all ncRNAs with significantly different slopes identified by the slope algorithm

5 Cleavage Algorithm Results

5.1 Features identified

5.1.1 Highest scoring tRNA fragments identified using the cleavage algorithm

Full results here:

  • ...Data/Cleavage_results/CytC_vs_TotalRNA_High-cleavage-tsRNAs.txt

5.1.2 Coverage plots for all tRNAs with irregular 5’ vs 3’ coverage identified by the cleavage algorithm

5.1.3 Highest scoring ncRNA fragments identified using the cleavage algorithm

Full results here:

  • ...Data/Cleavage_results/CytC_vs_TotalRNA_High-cleavage-ncRNAs.txt

5.1.4 Coverage plots for all ncRNAs with irregular 5’ vs 3’ coverage identified by the cleavage algorithm

6 Fisher’s Method Results

6.1 Feature identified

6.1.1 Highest scoring tRNA fragments identified using Fisher’s method

Full results here:

  • ...Data/FishersMethod_results/CytC_vs_TotalRNA_tsRNAs.low.p.values.txt

6.1.2 Coverage plots for all tRNAs with irregular distribution identified using Fisher’s method

6.1.3 Highest scoring ncRNA fragments identified using Fisher’s method

Full results here:

  • ...Data/FishersMethod_results/CytC_vs_TotalRNA_ncRNAs.low.p.values.txt

6.1.4 Coverage plots for all ncRNAs with irregular distribution identified using Fisher’s method

7 More results:

7.0.1 tRNA fragments identified where read origin accurate only to isoacceptor level

7.1 Other

7.1.1 All tRNA coverage plots can be found here:

  • ...Plots/CytC_vs_TotalRNA_Features_All-tsRNAs.pdf

7.1.2 Predicted tsRNA types

## Warning in file(file, "rt"): cannot open file '../Analyses_tsRNAsearch/
## ...Data/Predicted-tsRNA-types.tsv': No such file or directory
## Error in file(file, "rt"): cannot open the connection
Predicted tsRNA type
feature slope.score Fishers.method.pvalue distribution.score DESeq2.Log2FC DESeq2.pvalue DESeq2.padj cleavage.score
GlyGCC 314155.049 0.0000000 11277.364 NA NA NA NA
Val 303941.118 0.0000000 19074.385 NA NA NA 23687319.1
GlyCCC 152887.596 0.0000000 7592.334 NA NA NA NA
ENSMUSG00000092998 (Mir5099) 125730.003 0.0000000 36319.736 3.7560814 0.0000000 0.0000000 37234475.7
ValCAC 75219.156 0.0000002 4057.715 0.7499996 0.0630639 0.1322865 5101647.2
LysCTT 63856.215 0.2097641 3049.099 -0.0218859 0.9529760 0.9529760 46526580.9
GluCTC 47755.916 0.0000000 20639.234 0.0391343 0.9255359 0.9529760 13962563.2
ArgTCT 41106.248 0.0000000 113526.736 0.7225153 0.2330568 0.3088003 108859109.7
CysGCA 33049.813 0.0000000 27178.009 -3.8541300 0.0000008 0.0000084 4334959.1
LysTTT 27509.196 0.0000000 172910.160 4.4876410 0.0000000 0.0000001 10564825.0
ENSMUSG00000065922 (n-R5-8s1) 26371.763 0.1384756 43692.462 2.9885247 0.0000066 0.0000498 3576746.3
ArgCCT 22715.322 0.0000000 8334.162 -3.5036150 0.0001003 0.0005908 453341.1
ENSMUSG00000084667 (Gm23212) 16539.744 0.0000000 374364.238 6.8606585 0.0000023 0.0000205 1564417.7
HisGTG 13869.156 0.7752664 2547.189 NA NA NA NA
ENSMUSG00000064500 (Gm25296) 10361.264 0.0000000 120443.892 6.0657928 0.0001817 0.0009629 2563440.5
MetCAT 9392.816 0.0000000 2973.051 1.3402278 0.0976291 0.1784256 592825.1
ENSMUSG00000077797 (Snord19) 9111.062 0.0000000 140955.930 6.4161988 0.0000435 0.0002882 230098.7
AspGTC 6147.152 0.0000000 5508.929 -0.3292130 0.7588220 0.8378660 603522.5
ENSMUSG00000065378 (Gm22744) 6083.708 0.0000000 66405.980 5.2134472 0.0062729 0.0251689 328807.0
ENSMUSG00000064780 (Snord95) 5343.119 0.0000000 105037.467 4.9119721 0.0154228 0.0480828 959292.0

7.1.3 Run information

7.1.3.1 Date and time

Pipeline initiated at Fri Jun 26 12:53:51 IST 2020

Pipeline finished at Fri Jun 26 13:04:16 IST 2020

7.1.3.2 Parameters used

Parameters:
Species (-s): mouse
Input directory containing fastq/fastq.gz files (-d): ExampleData/
Input fastq/fastq.gz file (-f): NA
Experiment layout file (-e): additional-files/Example_ExperimentLayout.csv
Output directory (-o): ../Analyses_tsRNAsearch/Test_26-6-20
Number of threads used (-t): 5
Minumum read length (-l): 16
Plot all features (-A): no
Skip pre-processing (-S): no
Remove intermediate files (-R): yes

7.1.3.3 Version

tsRNAsearch version 0.26